ИСТИНА

Structural stability and other aspects of physical chemistry of quadruplex DNA are important issues for the pharmacological industry and modern biology. The formation and structural stability of Gquadruplexes depend on several factors, such as stacking interactions between nucleic acid bases, hydrogen bonds between them, electrostatic interactions and hydration shell. In addition, quadruplexes have also specific stability factors ones, namely, coordination of carbonyl oxygens by cations inside the G-DNA stems, and presence of connecting single-stranded loops in monomeric and dimeric G-DNA molecules (1, 2). Loops' length and sequence have a strong influence on G-quadruplex stability and folding efficiency (3,4). And also formation of quadruplexes requires cations (5,6). Location of cations inside of the quadruplex structure depends on cation size and charge. Na+ could be located in two positions: being sandwiched by the quartets, and in the plane of quartet. K+ and NH4 + are too large to fit into the second position, so that they are situated symmetrically in the center of quadruplex (7). Most of quadruplex structures have been solved with NMR which has limited capability to detect bound ions. In general, the current experimental techniques do not provide much information on details of structural dynamics of ion binding to G-DNA. In the study on thrombin aptamer (15-TBA), a combination of explicit solvent molecular dynamics simulation (30 simulations, 4 μs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-TBA. Binding of ions to G-DNA is complex multiple-pathway process, which is strongly affected by the cation nature. The individual ion binding events are effected by connecting loops, which play several roles. They stabilize the molecule during time periods when the bound ions are absent, they modulate the route of the ion into the G-stem, and they also stabilize, already coordinated ions by closing the gates through which the ions enter the quadruplex. Using extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution have been observed for the first time. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange.