Figure 2.
The building block of the Z-conformations are two distinct dinucleotide steps. (A) d(CpG)3 sequence in the Z-conformation (PDB: 7JY2 [33]). Z-form nucleic acids are composed of two distinct, overlapping dinucleotides steps. In both steps, ribose O4′ (red spheres) alternate between “pointing up” and “pointing down”. Pyrimidines adopt anti conformations and C3′-endo puckers, whereas purines adopt syn conformations and C2′-endo puckers. On the left, the Z-step (anti-p-syn) exhibits a unique contact not typically seen in other steps or helical conformations. One lone pair of oxygen O4′ sits within the vdW depression of the guanidinium system, resulting in lp···π contacts and close nucleobase plane distances. The other lone pair of oxygen O4′ facilitates an nO4 → σ*C6H hyperconjugation. The other step (syn-p-anti) does not include the lp···π contacts but does include the nO4 → σ*C6H hyperconjugation. (B) Top-down view of the CpG step. O4′ can be seen pointing into guanine’s six-membered ring close to C2 and the interstrand cytidine base stacking can also be seen. (C) Top-down view of the GpC step. There is no lp···π contact and only intrastrand base-stacking occurs.