Extended Data Fig. 6: Comparison of the original epoxide-biotin ligand and bromoalkyl-biotin counterparts reacting with a self-biotinylating ribozyme.
From: Engineering covalent small molecule–RNA complexes in living cells
a, Secondary structure of the RNA sequence used. Site of alkylation is indicated by red color. Other colors indicate secondary structure elements. b-d, Chemical structures of ligands used for the comparison of their alkylation efficiencies. e, The RNA alkylation reactions were analyzed by PAGE, blotting to a nylon membrane, and visualization with EtBr staining (before blotting, left) and AlexaFluor™ 647-streptavidin (after blotting, right). Br-C4-biotin resulted in higher yields compared to epoxy-biotin; hardly any RNA alkylation was observed for Br-C5-biotin. Results from one experiment are shown. f, RNA alkylation reactions analyzed by RP-HPLC (Supelcosil LC-18-S, gradient: 0-20% B in 40 min; buffer A: 50 mM triethylammonium acetate (TEAA) pH 7.0, buffer B: acetonitrile (ACN). HPLC traces for individual time points of the reaction are depicted. g, Graph shows relative conversion vs reaction time to determine reaction kinetics (see Supplementary Table 1).
