BASE-BASE AND DEOXYRIBOSE-BASE STACKING INTERACTIONS IN B-DNA AND Z-DNA - A QUANTUM-CHEMICAL STUDY

Base-stacking interactions in canonical and crystal B-DNA and in Z-DNA steps are studied using the ab initio quantum-chemical method with in clusion of electron correlation. The stacking energies in canonical B- DNA base-pair steps vary from -9.5 kcal/mol (GG) to -13.2 kcal/mol (GC ), The many-body nonadditivity term, although rather small in absolute value, influences the sequence dependence of stacking energy, The bas e-stacking energies calculated for CGC and a hypothetical TAT sequence in Z-configuration are similar to those in B-DNA. Comparison with old er quantum-chemical studies shows that they do not provide even a qual itatively correct description of base stacking. We also evaluate the b ase-(deoxy)ribose slacking geometry that occurs in Z-DNA and in nucleo tides linked by 2',5'-phosphodiester bonds. Although the molecular orb ital analysis does not rule out the charge-transfer n-pi() interactio n of the sugar 04' with the aromatic base, the base-sugar contact is s tabilized by dispersion energy similar to that of stacked bases. The s tabilization amounts to almost 4 kcal/mol and is thus comparable to th at afforded by normal base-base stacking. This enhancement of the tota l stacking interaction could contribute to the propensity of short d(C G)(n) sequences to adopt the Z-conformation.