The Relative Thermodynamic Stability of Base Stacking in Pyrimidine / Purine Dinucleotides

Consistent relative stacking interaction energies have been calculated for triply ionised dinucleotide structures in the g-gconformation. For UpAp, ApUp, CpAp and ApCp , the stacking energies in the ZKE approximation including zeropoint energies were found to be -0.031, -0.028, -0.033, -0.033 +/0.001 h, respectively. The corresponding free energy values at 298.15 K were found to be: -0.017, -0.007, -0.019, -0.014 +/0.001 h, respectively. For CpGp, GpCp, UpGp and GpUp , the stacking energies in the ZKE approximation including zero-point energies were found to be -0.046, -0.061, -0.035, -0.036 +/0.001 h, respectively. The corresponding free energy values at 298.15 K were found to be: -0.027, -0.037, -0.023, -0.034 +/0.001 h, respectively. These values enable the preferred structures of sequences to be determined in the nearest neighbor Ising model of a polyribonucleotide. The highest and lowest enthalpy values for pentamer nucleotides were recorded as UpUpUpUpUp = -0.105 h, and GpCpGpCpGp = -0.215 h A positive correlation is found between the frequencies of dinucleotides in 5S RNA and those calculated from the free energies of stacking for the dinucleotides. The stacking interactions were calculated for the overall enthalpy changes in the ZKE approximation at the HF and MP2 /6-31G* level. Key-Words: Thermodynamic data, base stacking, pyrimidine / purine dinucleotides, 5S RNA