Mechanism of unfolding and relative stabilities of G-quadruplex and I-motif noncanonical DNA structures analyzed in biased molecular dynamics simulations.

In this work we studied the unfolding processes of the noncanonical telomeric DNA fragments, i.e. G-quadruplex and i-motif. These transitions were analyzed in details by applying biased molecular dynamics simulations. The bias is imposed on the root of mean square displacement of selected atoms from the reference states which are ideal G-quadruplex and i-motif structures. The unfolding is carried out using the telomeric duplex fragment within which these both noncanonical structures are formed in the same place and exist together. The unfolding of one of the structures is carried out without affecting the second one. In the next stage of the studies the unfolding of the i-motif was also studied starting from the already unfolded G-quadruplex. We found that the work necessary to destroy G-quadruplexes are high at both acidic and neutral pH. The same was observed in the unfolding of i-motif at acidic pH. However, at the neutral pH the obtained work was small though still nonzero. It means that the presence of the complementary guanine rich strand enhances the stability of the i-motif which normally spontaneously unfolds to the hairpin at the neutral pH. Moreover, we found that unfolded G-quadruplex fragment is able to interact with the still existing i-motif and this leads to significant stabilization of the i-motif at the neutral pH. Thus, the presence of the complementary G-quadruplex at the neutral pH stabilizes the i-motif to some extent but even stronger stabilizing effect is observed after unfolding and relaxing the G-quadruplex.