AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments

Abstract

SUMMARY Aptamers, short RNA or DNA molecules that bind distinct targets with high affinity and specificity, can be identified using High Throughput Systematic Evolution of Ligands by Exponential Enrichment (HT-SELEX). But scalable analytic tools for understanding sequence-function relationships from diverse HT-SELEX data are not available. Here, we present AptaTRACE, a computational approach that leverages the experimental design of the HT-SELEX protocol, RNA secondary structure, and the potential presence of many secondary motifs to identify sequence-structure motifs that show a signature of selection. We apply AptaTRACE to identify nine motifs in C-C chemokine receptor type 7 targeted by aptamers in an in vitro cell-SELEX experiment. We experimentally validate two aptamers whose binding required both sequence and structural features. AptaTRACE can identify low-abundance motifs, and we show through simulations that because of this it could lower HT-SELEX cost and time by reducing the number of selection cycles required. AptaTRACE is available for download at www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#aptatools.

In Vitro Selection and Characterization of DNA Aptamers to a Small Molecule Target

“…The AptaTools software suite developed by the Przytycka group in 2014 allows users to cluster sequences into families based on sequence similarity, track changes in aptamer families by round, analyze sequence enrichment by round, and predict secondary structure (Dao et al, 2016;Hoinka et al, 2015;Hoinka, Berezhnoy, Sauna, Gilboa, & Przytycka, 2014;Hoinka, Zotenko, Friedman, Sauna, & Przytycka, 2012). The AptaTools software suite developed by the Przytycka group in 2014 allows users to cluster sequences into families based on sequence similarity, track changes in aptamer families by round, analyze sequence enrichment by round, and predict secondary structure (Dao et al, 2016;Hoinka et al, 2015;Hoinka, Berezhnoy, Sauna, Gilboa, & Przytycka, 2014;Hoinka, Zotenko, Friedman, Sauna, & Przytycka, 2012).…”

High-throughput methods in aptamer discovery and analysis

“…However, both of these methods are limited to identification of dominant motifs-an outcome that may not be desirable in selections for complex targets that are expected to yield multiple motifs, or in genomic SELEX, in which an exhaustive mapping of all aptamers is often preferred. AptaTrace overcomes this problem by tracing motifs through multiple rounds of selection data and testing whether these regions undergo selection toward secondary structure, such as hairpin loops or bulges (Dao et al, 2016). More recently, AptaSuite was developed as an all-encompassing software package, which includes AptaTrace and AptaCluster, and is the first open-source package designed for selection schemes to feature a graphical user interface (GUI) (Hoinka, Backofen, & Przytycka, 2018).…”

Applications of High-Throughput Sequencing for In Vitro Selection and Characterization of Aptamers

“…“AptaTrace” is another software that has been recently developed to identify structure motifs that are enriched during the SELEX [35]. Using SFOLD [36], predicted secondary structures are built for all sequences and a secondary structure probability profile is made for each nucleotide in the sequences.…”