Extended Data Fig. 8: Characterization of SiR RNA aptamers by focused UltraSelex.
From: Single-step discovery of high-affinity RNA ligands by UltraSelex
a, Consensus secondary structure of the SiR-A-like species in the top 7500 UltraSelex SiR-B library, containing the tetranucleotide UGAA (purple) in the loop and UAUC (green) in the bulge. In total, 1293 species harbor both tetranucleotides. b, Revised consensus secondary structure of the predominant species with a three base-pair stem embedding the UAUC tetraloop. c, Distribution of lengths and base pairing types of the stem embedding the UAUC loop of the RNA species in a and b. ‘|’ indicates a base pair (A–U, G–C and G–U), while ‘.’ symbolizes unpaired bases. The predominant stem type with three base pairs and two/four base pairs are shown in light and dark green, respectively, while the minor variants are depicted in blue. d, Detailed sequence information for the subgroup with a 3 bp-stem in c. Wobble pairs (G–U) are denoted by red color. ‘#’ symbolizes the UAUC loop. e, Correlation between the length of the stem embedding the ‘UAUC’ and the measured turn-on fluorescence and KD values. Seven UltraSelex SiR-B RNA aptamers containing the ‘UAUC’ motif are depicted with their ranking order. Symbols indicate different stem types. KD values above 2000 nM are shown as ‘2000 nM’. f, Abundance distribution of the UltraSelex SiR-B top 7500 RNA species in the mutagenized focused UltraSelex library. The left box plot panel illustrates (in triplicates) the distribution of these 7500 progenitor species from the original synthesized DNA library (input DNA) to mutagenesis PCR products, Taq PCR products to in vitro transcribed RNA. The right box plot panel shows the abundance of these progenitor species in the focused UltraSelex partitioning eluates (e1–11). The box pots are defined as in Fig. 2f.
