Dinucleotide hydration sites

M. Nekardová, L. Biedermannová, J. Černý, and B. Schneider

Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., BIOCEV, Průmyslová 595, 252 50 Vestec, the Czech Republic

ela.nekardova@gmail.com

 

Understanding of the biological function of DNA requires to understand its molecular structure. It is generally known that DNA is polymer made up of nucleotides that contain a phosphate group, a sugar group and a nitrogen base. The recurrent pattern of the sugar group and the phosphate group constitute the DNA backbone. DNA complexes are typically comprised of two or more strands. Functional forms of DNA are stabilized by base pairing, base stacking, and interactions with solvent. Influence of water molecules on the structure and function of DNA is an object of numerous researches [1, 2].

 

Our work is focused on the analysis of the relation between hydration sites and dinucleotide conformations. We used the previously published method [1] to identify the positions and intensities of the hydration sites of the defined dinucleotides conformational classes called NtC (Nucleotide Classes) [3]. The bioinformatic analysis is based on the crystal structures with a resolution better than 2.6 Å with the most frequent resolution being near 2.2 Å. The dinucleotides were classified into the NtC using the protocol [3] and further analysed separately for each of the 16 possible dinucleotide sequences. For the calculation of the average water positions, so called hydration sites [1], we took into account only the dinucleotides for which our database of available dinucleotide structures contains with more than 500 waters. The distributions of water molecules were expressed as pseudo-electron-density maps, and hydration sites were determined as maxima in the density map [1, 6]. The results will be presented in the Atlas of biomolecular hydration, Watlas, based on the recently published atlas of amino acid hydration [4, 5]. Here, we present results for selected NtC classes with the highest occupancy of water molecules.

 

1.         B. Schneider and H. M. Berman: Biophys J. 69, 2661-2669 (1995).

2.         B. Schneider, K. Patel and H. M. Berman: Biophys. J. 75, 2422-2431 (1996).

3.         Schneider, B., et al., Acta Crystallographica Section D-Structural Biology, 74, (2018), 52-64.

4.         L. Biedermannova and B. Schneider, Acta Crystallogr D Biol Crystallogr, 71, (2015), 2192-2202.

5.         J. Cerny, B. Schneider, L. Biedermannova: PCCP, 19, 17094 (2017).

5.         M. D. Winn et al., Acta Crystallogr D Biol Crystallogr, D67, (2011), 235-242.

 

The institutional support from the Institute of Biotechnology (RVO 86652036) is greatly acknowledged.