Structural transition from antiparallel to parallel G-quadruplex of d(G4T4G4) induced by Ca2+

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Abstract
Guanine quadruplex (G‐quadruplex) structures are formed by guanine‐rich oligonucleotides. Because of their in vivo and in vitro importance, numerous studies have been demonstrated that the structure and stability of the G‐quadruplex are dependent on the sequence of oligonucleotide and environmental conditions such as existing cations. Previously, we quantitatively investigated the divalent cation effects on the antiparallel G‐quadruplex of d(G4T4G4), and found that Ca2+ induces a structural transition from the antiparallel to parallel G‐quadruplex, and finally G‐wire formation. In the present study, we report in detail the kinetic and thermodynamic analyses of the structural transition induced by Ca2+ using stopped‐flow apparatus, circular dichroism, size‐exclusion chromatography (SEC) and atomic force microscopy. The quantitative parameters showed that at least two Ca2+ ions were required for the transition. The kinetic parameters also indicated that d(G4T4G4) underwent the transition through multiple steps involving the Ca2+ binding, isomerization and oligomerization of d(G4T4G4). The parallel‐stranded G‐wire structure of d(G4T4G4), which is a well controlled alignment of numerous DNA strands with G‐quartets, as the final product induced by Ca2+, was observed using SEC and atomic force microscopy. These results provide insight into the mechanism of the structural transition and G‐wire formation and are useful for constructing a nanomaterial regulated by Ca2+.