Single Base-Modification Reports and Locates Z-DNA Conformation on a Z-B-Chimera Formed by Topological Constraint

Abstract

Abstract Two complementary mini single-stranded DNA circles can hybridize with each other and form Z-B-chimera with a stable left-handed duplex part under low ionic strength conditions. However, we do not know clearly whether this left-handed part has Z-DNA conformation or a new left-handed one. In this study, 2′-OMe-thG, a fluorescent nucleobase, was introduced to detect the formation of Z-DNA conformation at a fixed point of sequence simply by measuring fluorescence change under various conditions. Results showed that the base pair at the modified site formed and the corresponding duplex structure took the Z-conformation in the Z-B-chimera. Z-DNA can form at low ionic strength such as 1.0 mM MgCl2, 75 mM NaCl or 140 mM KCl, which is lower than that of physiological ionic conditions. We also found that formation of Z-DNA becomes more difficult at lower pH (pH <6). This straightforward approach can be used to investigate Z-DNA formation by observing the fluorescence. Formation of Z-B-chimera can be used as a versatile tool to understand Z-DNA characteristics as well as its biological significance.