A single natural RNA modification can destabilize a U•A-T-rich RNA•DNA-DNA triple helix

EMSA results for modified 22-nt sequence from lncRNA AL157886.1 binding to D-D. (A) Table showing the R•D-D constructs and measured K_{D, EMSA} values for the AL157886.1 segment containing no modifications, a single m⁵C modification at three different sites, and three m⁵C modifications. Red nucleotides indicate the m⁵C location in each RNA. The putative Watson–Crick and Hoogsteen interactions are represented by a solid line (|) and a dot (•), respectively. The asterisk (*) denotes the location of the 5′-[³²P]-radiolabel. The reported K_{D, EMSA} values are average of at least three independent replicates and the associated standard deviation. (B) Bar plot showing the stability of each modified triple helix relative to the unmodified triple helix. The relative stability was calculated as K_{D, EMSA}(unmodified)/K_{D, EMSA}(modified). Error bars are the standard deviation of at least three independent experiments.