BIOINFORMATIC ANALYSES OF THE FIRST SOLVATION SHELL OF NUCLEIC ACIDS


Bohdan Schneider

 

Institute of Biotechnology AS CR, v.v.i., Vdesk 1083, CZ-142 20 Prague, Czech Republic; http://www.structbio.eu/BS/

 

Keywords: hydration, solvation, nucleic acids, DNA, RNA, structural bioinformatics

 

Relative humidity, quality and quantity of cations and other solvent species and solvation in general determine thermodynamic and structural behavior of nucleic acids. Structures determined by x-ray crystallography provide a unique information about the first solvation shells of biomolecules. We studied various aspects of the first solvation shell of DNA and RNA by analysis of distributions of water and metal cations around nucleotides in publically deposited crystal structures of nucleic acids. Detailed analysis of hydration in double helical DNA showed that their first hydration shell is well localized, stereochemistry of the preferred positions of water molecules around bases and phosphates, so called hydration sites, is determined locally, i.e. primarily by geometry of the hydrogen bond, but the exact location of the hydration sites adjusts to the nucleic acid conformation and sequence. This is in general true also for metal binding sites around phosphates but variability of their positions is lower than that of water positions and especially the magnesium binding site to the phosphate group is almost unchanged in DNA or RNA of various conformations. Hydration sites can serve as markers for optimal binding positions of hydrophilic drug and protein functional groups, and perhaps surprisingly, also to their hydrophobic groups.

Acknowledgements. The reviewed solvation projects have been mostly supported by NSF grants to the Nucleic Acid Database, NDB. The support of the Institute of Biotechnology AS CR, v.v.i. (AV0Z50520701) is acknowledged.