Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine

The ability of the four-stranded guanine (G)-DNA motif to incorporate nonst andard guanine analogue bases 6-oxopurine (inosine, I), 6-thioguanine (tG), and 8-thiopurine (tl) has been investigated using large-scale molecular dy namics simulations. The simulations suggest that a G-DNA stem can incorpora te inosines without any marked effect on its structure and dynamics. The al l-inosine quadruplex stem d(IIII)(4) shows identical dynamical properties a s d(GGGG)(4) on the nanosecond time scale, with both molecular assemblies b eing stabilized by monovalent cations residing in the channel of the stem. However, simulations carried out in the absence of these cations show drama tic differences in the behavior of d(GGGG(4), and d(IIII)(4). Whereas vacan t d(GGGG)(4) shows large fluctuations but does not disintegrate, vacant d(I III)(4) is completely disrupted within the first nanosecond. This is a cons equence of the lack of the H-bonds involving the N2 amino group that is not present in inosine. This indicates that formation of the inosine quadruple x could involve entirely different intermediate structures than formation o f the guanosine quadruplex, and early association of cations in this proces s appears to be inevitable. In the simulations, the incorporation of 6-thio guanine and 6-thiopurine sharply destabilizes four-stranded G-DNA structure s, in close agreement with experimental data. The main reason is the size o f the thiogroup leading to considerable steric conflicts and expelling the cations out of the channel of the quadruplex stem. The G-DNA stem can accom modate a single thioguanine base with minor perturbations. Incorporation of a thioguanine quartet layer is associated with a large destabilization of the G-DNA stem whereas the all-thioguanine quadruplex immediately collapses .