Structural Features of Intra- and Intermolecular G-Quadruplexes Derived from Telomeric Repeats

The 3′ strand of telomeres is composed of tandem repeats of short G-rich sequences which protrude as single-stranded DNA overhangs. These repeats are G₃T₂A in humans and G₄T₂ and G₄T₄ in the ciliates Tetrahymena and Oxytricha, respectively. We analyzed different quadruplex-forming sequences derived from telomeric sequences, G_3+k(T_n+kG_3+k)₃ and G_3+k(T₂AG_3+k)₃, in the presence of Li⁺, Na⁺, and K⁺ through the use of circular dichroism, UV spectroscopy, and electrophoresis, where k = 0 or 1 and n = 1−3. Results obtained under the given conditions can provide more detailed information about the quadruplex structure. The major findings are as follows. (i) G-Repeats in solution form a mix of topologically different structures; only G₃(T₂G₃)₃ and G₃(TG₃)₃ repeats preferentially form the parallel interstrand structure. (ii) The Tetrahymena repeat can form at least two intramolecular conformers with different strand orientations and levels of stability. (iii) G-Quadruplex conformation and molecularity strongly depend on the type and concentration of ions used in the solution. The formation of intramolecular quadruplexes is governed by the length of the loops connecting G-runs. Intermolecular G-quadruplex forms are more likely to form in a higher concentration of ions for sequences where G-runs are separated by only one or two nucleotides.