Open AccessOpposite Effects of Potassium Ions on the Thermal Stability of i-Motif DNA in Different Buffer Systems
Author(s) -
Bo Gao,
Xi Miao Hou
Publication year - 2021
Publication title -
acs omega
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.779
H-Index - 40
ISSN - 2470-1343
DOI - 10.1021/acsomega.0c06350
Subject(s) - chemistry , circular dichroism , dna , crystallography , buffer (optical fiber) , intercalation (chemistry) , förster resonance energy transfer , protonation , motif (music) , tris , thermal stability , molecule , ion , biophysics , fluorescence , biochemistry , inorganic chemistry , biology , organic chemistry , telecommunications , physics , quantum mechanics , computer science , acoustics
i-motifs are noncanonical DNA structures formed via the stack of intercalating hemi-protonated C + : C base pairs in C-rich DNA strands and play essential roles in the regulation of gene expression. Here, we systematically investigated the impacts of K + on i-motif DNA folding using different buffer systems. We found that i-motif structures display very different T m values at the same pH and ion strength in different buffer systems. More importantly, K + disrupts the i-motif formed in the MES and Bis-Tris buffer; however, K + stabilizes the i-motif in phosphate, citrate, and sodium cacodylate buffers. Next, we selected phosphate buffer and confirmed by single-molecule fluorescence resonance energy transfer that K + indeed has the stabilizing effect on the folding of i-motif DNA from pH 5.8 to 8.0. Nonetheless, circular dichroism spectra further indicate that the structures formed by i-motif sequences at high K + concentrations at neutral and alkaline pH are not i-motif but other types of higher-order structures and most likely C-hairpins. We finally proposed the mechanisms of how K + plays the opposite roles in different buffer systems. The present study may provide new insights into our understanding of the formation and stability of i-motif DNA.