Thermodynamic characteristics for the formation of H-bonded DNA base pairs

Abstract

Thermodynamic characteristics for the formation of gas-phase H-bonded DNA base pairs were evaluated using ab initio data (geometries and vibrational frequencies of bases and base pairs and base pair stabilization energies) utilizing the rigid rotor - harmonic oscillator - ideal gas approximations. While the stabilization energies for various DNA base pairs differ considerably (by more than 200%), the respective entropy terms are more uniform and vary by less than 40%. Calculated values are compared with experimental interaction enthalpies and equilibrium constants obtained from field-ionization mass spectrometry and supersonic beam experiments, respectively. The agreement in the former case was good, while in the latter, a deep disagreement was found; the validity of supersonic beam experiments is argued. Equilibrium constants for the formation of DNA base pairs obtained by the free energy perturbation/molecular dynamics method differ from the respective ab initio values.