Extended Data Fig. 10: Discovery of 2′-F-modified RNA aptamers that inhibit HIV-1 reverse transcriptase by UltraSelex.
From: Single-step discovery of high-affinity RNA ligands by UltraSelex
a, Inhibition of template extension by HIV-1 reverse transcriptase (RT, HXB2; Addgene, 153311) using UltraSelex-derived 2′-F-modified RNA aptamers. An 18-nt fluorescent 5′-Cy3-labeled DNA primer (10 nM) and 31-nt DNA template (100 nM)31 were incubated with the indicated 2′-F CTP/UTP-modified RNA aptamer (10 nM) and RT (10 nM) for 15 min. Controls included reaction without RT (-Enzyme), RNA aptamer (PC), or dNTP (-dNTP), while the reported unmodified strong broad spectrum of RT inhibitor unmodified RNA 70N89 (ref. 31) served as reference. Selected 2′-F-modified RNA aptamers containing GCCU and CGGG motifs32 were designated as the ‘cg’ group. b, Quantification of the inhibition effect from a. The gray dashed line represents the inhibition level of 70N89 aptamer. RNA aptamers with more than 10% inhibition (high) are marked with an asterisk (*), while those with similar inhibition to 70N89 were classified as ‘intermediate’ group. Error bars represent the mean ± s.d. from technical triplicates. c, Consensus secondary structure of RNA aptamers with ‘high’ inhibition in b using LocARNA26 alignment with default parameters. Degenerated bases are annotated as in Extended Data Fig. 9b. d, Alignment annotated with the LocARNA26 consensus structure of the ‘high’ (top) and ‘intermediate’ group (bottom) from b. The percentage of inhibition higher than 70N89 is shown in the last column. e, Predicted secondary structure of the RNA aptamer RT-F6, which exhibited the highest inhibition capability, using Mfold42 with default parameters. f, Box plot distribution of normalized AUC values of RT RNA aptamers from b. The AUC value with the weight of heptamer was min–max normalized into range between 0 and 1. The box plot is defined as in Fig. 2f.
