PH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs.

ABSTRACT: We study here a DNA oligonucleotide having the ability to form two different i-motif structures whose relative stability depends on pH and temperature. The major species at neutral pH is stabilized by two C:C⁺ base pairs capped by two minor groove G:C:G:C tetrads. The high pH and thermal stability of this structure are mainly due to the favorable effect of the minor groove tetrads on their adjacent positively charged C:C⁺ base pairs. At pH 5, we observe a more elongated i-motif structure consisting of four C:C⁺ base pairs capped by two G:T:G:T tetrads. Molecular dynamics calculations show that the conformational transition between the two structures is driven by the protonation state of key cytosines. In spite of large conformational differences, the transi

SUBMITTER: Serrano-Chacon I 

PROVIDER: S-EPMC9936585 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature