In Z-DNA, guanine bases have a syn glycosidic bond conformation. This describes the orientation of a guanine base relative to its deoxyribose sugar around the glycosidic bond connecting them.
The syn arrangement is a key reason Z-DNA differs from B-DNA. In the Z-DNA repeating structure, cytosine generally retains an anti conformation, while guanine flips into syn. This alternating pattern helps produce the helix’s unusual zigzag phosphate backbone and left-handed twist.
The distinction is structural, not a different kind of chemical bond. Syn and anti describe the spatial orientation of the nucleobase around the sugar; they do not mean that guanine is attached by a special bond in Z-DNA. A frequent error is to assume that all bases in DNA use the same orientation. In ordinary B-DNA, both purines and pyrimidines are typically anti, whereas Z-DNA’s guanine residues are notable for adopting syn.
Alternating guanine–cytosine sequences are especially associated with Z-DNA formation, although changes in salt, supercoiling, and protein binding also influence whether the conformation appears.