G-Quadruplex structure can be stable with only some coordination sites being occupied by cations: a six-nanosecond molecular dynamics study

Abstract

Guanine tetrads are formed spontaneously by guanine rich sequences in the presence of certain cations. Various quadruplex helical structures, stabilized by such tetrads, apparently play an important biological role in vivo. To understand the importance of the cations, a 6 ns molecular dynamics simulation has been performed on a 7-mer G-quadruplex, surrounded by Na⁺ counterions and explicit water molecules, but without any ions in the initial structure. Interestingly, the quadruplex structure does not fall apart, but undergoes small structural changes, which enable the solvent molecules, including Na⁺ ions, to enter the empty central channel of structure. This channel is fully hydrated within the first 100 ps and two ions move into the central channel between 0.5 and 2 ns of MD simulation, by replacing some of the water molecules. The ions once trapped within the quadruplex channel are not expelled even during 1.5 ns of MD at 400 K. In fact they penetrate deeper into the channel to facilitate entry of additional ions, though all coordination sites within the quadruplex are not occupied even after 6.1 ns of MD simulation. The entry of cations into the central channel leads to a quadruplex structure with more favorable free energy of hydration, which is comparable to that of a fully coordinated quadruplex.