Computational analysis of G-quadruplex in structural transition process driven by cation types
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Single-stranded DNA are highly flexible and can form a variety of conformations depending on conditions. Recent evidence suggests that the G-quadruplex (G4) is involved in numerous key genomic functions. The cations located in the core have attracted the attention with respect to their structural stability. Nevertheless, due to limitations in resolution, detailed mechanisms of ion-dependent conformational changes have not yet been reported. Here, we performed molecular dynamics simulations using two determined G4 structures with identical sequences but different cations to elucidate the mechanisms of structural change. Using enhanced sampling, we explored the structural space between two structures to collect numerous hybrid structures with their stability and observed preferences based on cation type. We aimed to identify the driving forces behind the transition by decomposing structural and energetic properties to characterize the key factors involved in folding/unfolding processes.