Cation-dependent conformational switches in d-TGGCGGC containing two triplet repeats of fragile X syndrome: NMR observations

Higher ordered structures formed by different DNA sequences have been widely investigated in recent years because of their implications in a variety of biological functions. Among these, G-quadruplexes have exhibited a great variety depending on the exact sequence, the lengths of the G-stretches, interception by other nucleotides, and environmental conditions such as pH, temperature, salt type, and its concentration. We report here interesting conformational switches observed by NMR in the sequence d-TGGCGGC containing two GGC triplet repeats related to the disease Fragile X-Syndrome. At neutral pH, the solution structure is a parallel-stranded quadruplex in presence of K+ ions. Lowering the pH does not cause a major change in the structure; however, the chemical shift patterns of the C4 and G3 base protons suggest protonation of the C-tetrad in the center of the quadruplex. In contrast, the sequence forms an antiparallel duplex in Na+ containing solutions. As the pH of the Na+ sample is lowered, an equilibrium mixture of a duplex and a quadruplex appears, and at pH 2.2, the molecule exists entirely as a quadruplex. These results would be of significance from the point of view of recognition and regulation by different helicase enzymes, which have been found to discriminate between different types of quadruplex structures