Combining independent protein and cellular SELEX with bioinformatic analysis may allow high affinity aptamer hit discovery

Ducrot, Coline; Piffoux, Max

doi:10.1016/j.omtn.2023.06.011

Cited by 1 publication

(1 citation statement)

References 8 publications

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“…al. (13) applied AptamerRunner to examine the relatedness of aptamer libraries enriched in two independent SELEX processes: a protein-based SELEX using recombinant human EphA2 as target and a Cell-Internalization SELEX using EphA2-expressing MDA231 cells as targets (13,37). The AptamerRunner clustering algorithm identified a group of aptamers within these two different SELEX processes that shared structure and sequence relatedness.…”

Section: Discussionmentioning

confidence: 99%

AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers

Ruiz-Ciancio,

Veeramani,

Embree

et al. 2023

Preprint

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Aptamers are short single-stranded DNA or RNA molecules with high affinity and specificity for targets and are generated using the iterative Systematic Evolution of Ligands by EXponential enrichment (SELEX) process. Next-generation sequencing (NGS) revolutionized aptamer selections by allowing a more comprehensive analysis of SELEX-enriched aptamers as compared to Sanger sequencing. The current challenge with aptamer NGS datasets is identifying a diverse cohort of candidate aptamers with the highest likelihood of successful experimental validation. Herein we present AptamerRunner, an aptamer clustering algorithm that generates visual networks of aptamers that are related by sequence and/or structure. These networks can then be overlayed with ranking data, such as fold enrichment or data from scoring algorithms. The ability to visually integrate data using AptamerRunner represents a significant advancement over existing clustering tools by providing a natural context to depict groups of aptamers from which ranked or scored candidates can be chosen for experimental validation. The inherent flexibility, user-friendly design, and prospects for future enhancements with AptamerRunner has broad-reaching implications for aptamer researchers across a wide range of disciplines.GRAPHICAL ABSTRACT

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Section: Discussionmentioning

confidence: 99%