To improve the previous DNA/DNA nearest-neighbor parameters, thermodynamic parameters (Δ H °, Δ S ° and Δ G °) of 50 DNA/DNA duplexes were measured. Enthalpy change of a helix initiation factor is also considered though the parameters reported recently did not contain the factor. A helix initiation factor for DNA/DNA duplex determined here was the same as that of RNA/RNA duplex (ΔG° 37 = 3.4 kcal/mol). The improved nearest-neighbor parameters reproduced not only these 50 experimental values used here but also 15 other experimental values obtained in different studies. Comparing Δ G ° 37 values of DNA/DNA nearest-neighbor parameters obtained here with those of RNA/RNA and RNA/DNA, RNA/RNA duplex was generally the most stable of the three kinds of duplexes with the same nearest-neighbor sequences. Which is more stable between DNA/DNA and RNA/DNA duplexes is sequence dependent.

The effects of counter ion on a nucleic acid duplex stability were investigated. Since a linear free energy relationship for the thermostability of oligonucleotide duplexes between those in 1 M and in 100 mM NaCl-phosphate buffer were observed regardless of whether they are DNA—DNA, RNA—RNA or RNA—DNA duplexes, simple prediction systems for ΔG°₃₇ as well as T_m values in 100 mM NaCl-phosphate buffer were established. These predictions were successful with an average error of only 2.4°C for T_m and 5.7% for G°₃₇ values. The number of Na⁺ newly bound to a duplex when the duplex forms (−Δn) was significantly influenced by the base composition, and −Δn for diGCCAGTTAA)/d(TTAACTGGC) was different for MgCI₂, CaCI₂, BaCI₂ and MnCI₂ (from 0.70 to 0.76 with the same order of the duplex stability). Almost no additive effects on the duplex stability was observed for NaCl and MgCI₂, suggesting a competitive binding for these cations. The sequence-dependent manner of Δn suggests the presence of preferential base pairs or nearest-neighbor base pairs for the cation binding, which would affect nearest-neighbor parameters.

We now present the first example in which triplet repeat DNAs adopt the i-motif structure at neutral pH by molecular crowding. Crowding stabilized the i-motif and the pK_a of N3 of cytosine was raised in such a microenvironment. Molecular crowding is known to accelerate the formation of the multi-stranded i-motif while the triplet repeats adopt the single-strand structure.

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⁺.