Influence of 3′–3′ inversion of polarity site within d(TGGGGT) on inter quartet cation binding

• d(5′TGG3′–3′GGT5′) forms tetramolecular G-quadruplexes in the presence of NH4+ ions.
• 3′–3′ inversion of polarity site influence binding of cations.
• Binding sites involving natural 5′–3′ backbone exhibit higher occupancy by cations.

Stability, dynamics and function of nucleic acids are affected by nature of cations that are involved in interaction with specific functionalities. Introduction of inversion of polarity sites represents a very useful and chemically accessible backbone modification, which can alter the binding affinity of cations. NMR study on cation binding between G-quartets in tetramolecular G-quadruplex adopted by d(5′TGG3′–3′GGT5′) with 3′–3′ inversion of polarity sites in the middle of G-tract showed existence of two different G-quadruplex forms with all strands in parallel orientation, where all guanine residues adopt anti conformation around glycosidic bonds in the presence of 15NH4+ ions. In one of the forms all three binding sites are equally populated, while in the second form the binding site next to the inversion of polarity site is not fully populated by 15NH4+ ions.

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