Structure of a C-rich strand fragment of the human centromeric satellite III: a pH-dependent intercalation topology

Stability of the I-motif structure is related to the interactions between phosphodiester backbones

The i-motif DNA tetrameric structure is formed of two parallel duplexes intercalated in a head-to-tail orientation, and held together by hemiprotonated cytosine pairs. The four phosphodiester backbones forming the structure define two narrow and wide grooves. The short interphosphate distances across the narrow groove induce a strong repulsion which should destabilize the tetramer. To investigate this point, molecular dynamics simulations were run on the [d(C2)]4 and [d(C4)]4 tetramers in 3'E and 5'E topologies, for which the interaction of the phosphodiester backbones through the narrow groove is different. The analysis of the simulations, using the Molecular Mechanics Generalized Born Solvation Area and Molecular Mechanics Poisson-Boltzmann Solvation Area approaches, shows that it is the van der Waals energy contribution which displays the largest relative difference between the two topologies. The comparison of the solvent-accessible area of each topology reveals that the sugar-sugar interactions account for the greater stability of the 3'E topology. This stresses the importance of the sugar-sugar contacts across the narrow groove which, enforcing the optimal backbone twisting, are essential to the base stacking and the i-motif stability. Tighter interactions between the sugars are observed in the case of N-type sugar puckers.

Characterization and thermodynamic properties of quadruplex/duplex competition

Structural characteristics and thermodynamic properties of dG(3)(T(2)AG(3))(3), d(C(3)TA(2))(3)C(3) and dG(3)(T(2)AG(3))(3)/d(C(3)TA(2))(3)C(3) were intensively investigated. It was indicated that metal ions greatly affected the conformation and stability of the G-quadruplex. A competition of a structure transition among the G-quadruplex, I-motif, and the duplex was confirmed to be dependent on both cation species and pH values. The structural competitive mechanism is discussed for the first time. This study shows an intriguing potential in modulating DNA structures in vivo, which is of great importance in drug design and cancer chemotherapy.