Free energy component analysis: application to the “Z-Phobicity” of A · T base pairs

Abstract

We have carried out molecular dynamics/free energy perturbation calculations on the double helical hexamer d(CGCGCG)₂ in both B and Z forms. The third C · G base pair was “mutated” to T · A in both B and Z-DNA. It is known experimentally that replacement of a C·G with a T·A base pair in an alternating CG sequence raises the energy of the Z form relative to the B form by ∼ 1 kcal mole⁻¹. We have carried out free energy component calculations to assess the reason for the “Z-phobicity” of T·A base pairs. There are two major contributions. The primary contribution is from the intra-base pair interactions of the mutated base pair itself which disfavor T·A relative to C·G in the Z form by ≃ 1.4 kcal mole⁻¹. A secondary contribution of 0.4 kcal mole⁻¹ arises because the two cytosines on the strand where G is mutated to A disfavor T·A relative to C·G in the Z form by 1.9 kcal mole⁻¹, while the guanines flanking the Con the complementary strand stabilize the T·A base pair relative to the C·G in the Z form by 1.5 kcal mole⁻¹. The effect of the phosphates, non-neighboring nucleotides and intramolecular energies of the base pair being mutated are all small and come close to canceling each other, leading to a net calculated free energy for T·A Z- phobicity of 1.7 kcal mole⁻¹.