The zeta potential is commonly referred to as surface charge density and is a key factor in modulating the structural and functional properties of nucleic acid. Although the negative charge density of B-DNA is well understood, there is no prior description of the zeta potential measurement of Z-DNA. In this study, we demonstrated the difference between zeta potential of B-DNA and lanthanum chloride-induced Z-DNA. A series of linear repeat i.e. (CG)n/(GC)n DNA as well as branched DNA (b-DNA) structures was used for the B-to-Z DNA transition. Herein, the positive zeta potential of Z-DNA has been demonstrated as a powerful tool to discriminate the conformational B-Z transition. The generality of the approach has been validated both in linear and self-assembled DNA nanostructures. Thus, we suggest zeta potential can be used as an ideal signature for the left-handed Z-DNA.