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

EMSA results for candidate lncRNA•gDNA triple helices. (A) R•D-D schematics show sequences and modification sites (red) of the 22-nt segments from the three lncRNAs examined: AC068025.2 (TAOK1), AL157886.1, and LINC00940. 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. (B) Representative gel images of dsDNA (D-D) and unmodified 22-nt segments from the three lncRNAs examined. Only the AL157886.1 segment (center) shows a shift from dsDNA (D-D) to triple helix (R•D-D) as increasing amounts of RNA are added. No binding to dsDNA was observed for the AC068025.2 (TAOK1) and LINC00940 segments (left and right, respectively). The K_{D, EMSA} value measured for AL157886.1•dsDNA is the average of four independent replicates and the associated standard deviation.