PMC

Native gel-shift assays of METTL16 binding to the MALAT1 triple helix in the absence or presence of RNA modifications.A–D, representative gel images of METTL16 binding to the (A) unmodified MALAT1 triple helix, (B) m⁶A-modified MALAT1 triple helix, (C) Ψ-modified MALAT1 triple helix, and (D) m¹Ψ-modified MALAT1 triple helix. E, representative binding plots of METTL16 for the unmodified MALAT1 triple helix (black), m⁶A-modified MALAT1 triple helix (magenta), Ψ-modified MALAT1 triple helix (blue), and m¹Ψ-modified MALAT1 triple helix (green). F, measurements of apparent equilibrium dissociation constant (K_D,app) between METTL16 and RNA with degrees of cooperativity (n). Data were fitted to the Hill equation (Equation ). Binding reactions that did not reach saturation for an accurate measurement of K_D,app are denoted as larger than the extrapolated K_D,app value. Measurements are reported as average ± standard deviation of three independent replicates. m¹Ψ, N¹-methylpseudouridine; m⁶A, N⁶-methyladenosine; Ψ, pseudouridine; MALAT1, metastasis-associated lung adenocarcinoma transcript 1; METTL16, methyltransferase-like protein 16.

The SAM-II triple helix. (a) Schematic depiction of the SAM-II riboswitch structure. The triple helix is shown as yellow, red, and orange nucleotides. Watson-Crick interactions are shown with solid lines whereas nonconventional and Hoogsteen base interactions within the triple helix are shown with solid circles. Tertiary interactions and nonconventional base pairs outside the triple helix are shown with dashed lines. SAM is blue (A_SAM), and the Shine-Delgarno sequence (A47–G52) is shaded with a green box. (b) Surface representation of the SAM-II riboswitch. The three strands corresponding to the triple helix and SAM are color coded as in (a). All structures for SAM-II were from PDB ID: 2QWY. (c) Stick representation of the triple helix domain in the SAM-II riboswitch showing the fit of SAM in the ligand-binding pocket. The three strands corresponding to the triple helix and SAM are color coded as in (a). (d) Base triples and hydrogen bonds between the SAM-II triple helix and the SAM adenosine. Nitrogens are dark blue, oxygens are bright red, hydrogens are white, carbons are color coded by triple helix strand as in (a). Hydrogen bonds are shown with dashed lines.

(A) Structure of a prototypical triple collagen fiber, adapted from Bella et al. Within the triple helix motif of alpha-1 collagen proteins, repeating triples of glycine-X-Y, where X is typically a hydroxylated proline and Y is proline, is thought to account for triple helix stability, with glycine occupying the crowded center of the three-stranded helix. (B) Substituting arginine for glycine destabilizes the triple helix by causing steric hindrance between the arginine side chain and the nearby amino acid side chains within the other two strands. Many types of substitutions within the triple helix motif from glycine can disrupt the stability of the triple helix through steric hindrance.

Triple helix in telomerase RNA. Telomerase RNA forms a nearly continuous triple helix (tricolor cartoon representation) in which a U•A‐U major‐groove triple helix is adjacent to a minor‐groove triple helix