Book of Abstracts: Albany 2005
Quantum-chemical Semiempirical Study of Bounded Water and Counter Ions in Structure-vibrational Organization of Short Oligonucleotide Duplexes
It is well known that interaction of charged sugar-phosphate backbone with counter-ions plays substantial role in the structural-dynamical organization of DNA molecule. This interaction in considerable degree determines peculiarities of stacking of H-bonded nucleotide pairs and vibrational dynamics of double helix.
In this work on the example of hydrating forms of short oligonucleotide duplexes with AT and GC types of pairing the role of water environment and counter ions of alkali elements Na+ and K+ on thermodynamic stability of H-bonding of nucleotides was theoretically studied. We analyzed the influence of metal ions on characteristics of equilibrium vibrational dynamics of hydrated duplexes.
To study electronic structure of duplexes we used PM3 technique of MOPAC7.01 program package. To take into account effect of bounded water and cations of metals we used ?supermolecule? approximation.
We showed that hydration of negatively charged duplexes modifies geometry of H-bonding of base-pairs. Moreover, different amounts of bounded water initiate different nonplanar forms of Watson-Crick base-pairs H-bonding. However, in the presence of counter ions of alkali metals near phosphate groups the geometry of H-bonding stays practically unchanged.
We found that collective modes of bounded water are the lowest vibrations, vibrations of hydrated forms of Na+ and K+ cations being among these modes. Noticeable activity of collective vibrational modes of nucleotides are found in the region of 20-30 cm-1.
1Institute of Cell Biophysics RAS