Two opposing effects of monovalent cations on the stability of i-motif structure

ABSTRACT At acidic pH, cytosine-rich single-stranded DNA can be folded into a tetraplex structure called i-motif (iM). In recent studies, the effect of monovalent cations on the stability of iM structures has been addressed, but a consensus about the issue has not been reached yet. Thus, we investigated the effects of various factors on the stability of iM structures using fluorescence resonance energy transfer (FRET)-based analysis for three types of iM derived from human telomere sequences. We confirmed that the iM structure is destabilized as the concentration of monovalent cations (Li + , Na + , K + ) increases and that Li + has the greatest tendency of destabilization. This cation-induced destabilization is rather unexpected and specific to the iM structure, considering the cation’s electrostatic effect of supporting DNA folding. Monovalent cations of different kinds promote the flexibility of single-stranded DNA (ssDNA) and the stability of folded DNA structures to different degrees, suggesting that the size of cation be a key factor in its function. All taken together, we conclude that the stability of iM structures is controlled by the subtle balance of the two counteractive effects of monovalent cations, electrostatic screening and disruption of cytosine base pairing.