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 approximately 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 congruent to 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 C on 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.