Conformational polymorphism and extensibility of DNA quadruplexes formed by d(GT)(n) repeats

We showed earlier that oligonucleotides 3'-d(GT)(5)-pO(CH2CH2O)(3)p-d(GT)(5 )-3' form bimolecular quadruplexes with parallel orientation of their stran ds, which are held by guanine quartets alternating with unpaired thymines ( GT quadruplex). This work deals with the conformational polymorphism and ex tensibility of G quadruplexes in complex with molecules of an intercalating agent ethidium bromide (EtBr). A cooperative mechanism of EtBr binding to the GT quadruplex was revealed. The binding constant K = (3.3 +/- 0.1)(.)10 (4) M-1, cooperativity coefficient omega = 2.5 +/- 0.2, and maximal amount of EtBr molecules intercalated in GT quadruplex (N = 8) were determined. It was proved experimentally by analysis of adsorption isotherms and theoreti cally by mathematical modeling that the GT quadruplex is capable of double extension, which is indicative of the high elasticity of this four-stranded helix. Two most stable conformations of GT quadruplexes with thymine resid ues intercalated and/or turned outside were found by mechanico-mathematical modeling. The equilibrium is shifted toward the conformation with the loop ed out thymine residues upon intercalation of EtBr molecules into the GT qu adruplex.