Intramolecular flexibility of DNA bases in adenine-thymine and guanine-cytosine Watson-Crick base pairs

The conformational flexibility of pyrimidine rings in adenine (A)-thymine (T) and guanine (G)-cytosine (C) Watson-Crick base pairs was investigated at the ab initio Hartree-Fock (HF) level using 6-31G** basis set. Transition of these rings from the planar equilibrium conformation to a distorted sofa conformation with torsion angles of 20 degrees results in a marginal energy increase of approximately 1.3 kcal/mol for the A-T pair and 3.5 kcal/mol for the G-C pair. In the GC pair, the simultaneous deformation of both pyrimidine rings was applied. Comparison of ring deformation energies calculated at the HF, with correlated levels indicates significant overestimation (up to 30%) of ring rigidity by the HF approximation. Reasonable correlations were found between the out-of-plane ring vibrational frequencies and the ring deformation energies. Formation of Watson-Crick base pairs is manifested in prolongation of the N-H bonds within the bases which results in significant reduction of the N-H stretching frequencies. On the basis of the calculated increase in the C-H stretching frequency of adenine, the existence of a third hydrogen bond of the C-H ... O type in the A-T pair is ruled out. (C) 1999 Elsevier Science B.V. All rights reserved.