STRUCTURE OF THE DNA SOLVATION SHELL

Bohdan Schneider^1,2 and Helen M. Berman²

¹J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, CZ-18223 Prague, Czech Republic
²Rutgers University, Department of Chemistry, Piscataway, NJ 08854-8087, USA

Keywords: DNA hydration, DNA solvation, metal - DNA interactions, recognition

Properties of DNA - its conformations as well as interactions with other molecules - are strongly influenced by the environment. Water and counterions in the first solvation shell are of particular importance for intermolecular interactions and recognition.

The talk will discuss our database studies of DNA solvation. Water as well as metal cations preferentially bind into sterically well defined sites around both bases [1, 2] and phosphates [3, 4]. Positions and occupancies of these sites vary between DNA conformational types and may indeed contribute to specificity of interactions with other molecules [5]. These hydrophilic binding sites are probable markers for binding of other ligands, from proteins regulating gene functions to antisense drugs.

The studies were based on analyses of crystal data. To analyze 3-D point like distributions of water and metals around DNA, we developed a method based on Fourier averaging [6] which displays distributions as densities and is more efficient than majority of traditional statistical methods.

1. B. Schneider & H.M. Berman: Biophys. J. 69, 2661-2669 (1995).
2. A. Harper et al.: Acta Cryst. D54, in press (1998).
3. B. Schneider & M. Kabelac: J. Am. Chem. Soc. 120, 161-165 (1998).
4. B. Schneider, K. Patel & H.M. Berman: Biophys. J., accepted (1998).
5. J. Woda, B. Schneider, K. Patel, K. Mistry & H.M. Berman: Biophys. J., accepted (1998).
6. Schneider, D. M. Cohen, L. Schleifer, A. R. Srinivasan, W. K. Olson & H.M. Berman: Biophys. J. 65, 2291-2303 (1993).