"CompELS: A Nonevolutionary Screening Approach for DNA Aptamers"
Valeria Milam, Ph.D.
Oligonucleotide aptamers are single-stranded sequences that exhibit high affinity and specificity for a particular nonnucleotide target. To date, aptamer studies typically entail an evolutionary-based screening approach called "Systematic Evolution of Ligands by EXponential Enrichment" (SELEX). SELEX has revolutionized the discovery of numerous DNA and RNA-based aptamers and dominated the field for over two decades as a screening approach; however, SELEX itself is a labor-intensive process with pitfalls such as its propensity to introduce PCR-based sequence bias and contaminants. Here, we have developed a nonevolutionary screening approach we call CompELS (Competition Enhanced Ligand Selection) to rapidly and reliably identify single-stranded DNA aptamers for a model target, namely gold. Following aptamer selection against our target we then evaluated winning sequences to identify base segment consensus as well as any shared and unshared patterns in their predicted secondary structure elements such as hairpins, internal loops, and multi-branched loops. Lastly, in a separate post-screening competition experiment, we ranked our aptamer candidates in terms of their frequency as a bound species using next generation sequencing and identified multiple high affinity aptamers. As aptamers continue to be pursued as potential ligands or capture agents in the biology and bioengineering community, our ongoing and future efforts include adapting our unconventional screening approach to enable faster and easier aptamer identification for challenging biological targets.