10.1021/bi902099u.s001 Viktor Víglaský Viktor Víglaský Luboš Bauer Luboš Bauer Katarína Tlučková Katarína Tlučková Structural Features of Intra- and Intermolecular G-Quadruplexes Derived from Telomeric Repeats American Chemical Society 2010 solution Intermolecular sequence 3T G 4T UV intramolecular strand DNA concentration Tetrahymena ion 2010-03-16 00:00:00 Journal contribution https://acs.figshare.com/articles/journal_contribution/Structural_Features_of_Intra_and_Intermolecular_G_Quadruplexes_Derived_from_Telomeric_Repeats/2784085 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 G<sub>3</sub>T<sub>2</sub>A in humans and G<sub>4</sub>T<sub>2</sub> and G<sub>4</sub>T<sub>4</sub> in the ciliates <i>Tetrahymena</i> and <i>Oxytricha</i>, respectively. We analyzed different quadruplex-forming sequences derived from telomeric sequences, G<sub>3+<i>k</i></sub>(T<sub><i>n</i>+<i>k</i></sub>G<sub>3+<i>k</i></sub>)<sub>3</sub> and G<sub>3+<i>k</i></sub>(T<sub>2</sub>AG<sub>3+<i>k</i></sub>)<sub>3</sub>, in the presence of Li<sup>+</sup>, Na<sup>+</sup>, and K<sup>+</sup> through the use of circular dichroism, UV spectroscopy, and electrophoresis, where <i>k</i> = 0 or 1 and <i>n</i> = 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 G<sub>3</sub>(T<sub>2</sub>G<sub>3</sub>)<sub>3</sub> and G<sub>3</sub>(TG<sub>3</sub>)<sub>3</sub> repeats preferentially form the parallel interstrand structure. (ii) The <i>Tetrahymena</i> 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.