Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery

Jan Hoinka, Alexey Berezhnoy, Phuong Dao, Zuben E. Sauna, Eli Gilboa, Teresa M. Przytycka

Research output: Contribution to journalArticle

45 Scopus citations

Abstract

High-Throughput (HT) SELEX combines SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a method for aptamer discovery, with massively parallel sequencing technologies. This emerging technology provides data for a global analysis of the selection process and for simultaneous discovery of a large number of candidates but currently lacks dedicated computational approaches for their analysis. To close this gap, we developed novel insilico methods to analyze HT-SELEX data and utilized them to study the emergence of polymerase errors during HT-SELEX. Rather than considering these errors as a nuisance, we demonstrated their utility for guiding aptamer discovery. Our approach builds on two main advancements in aptamer analysis: AptaMut - a novel technique allowing for the identification of polymerase errors conferring an improved binding affinity relative to the 'parent' sequence and AptaCluster - an aptamer clustering algorithm which is to our best knowledge, the only currently available tool capable of efficiently clustering entire aptamer pools. We applied these methods to an HT-SELEX experiment developing aptamers against Interleukin 10 receptor alpha chain (IL-10RA) and experimentally confirmed our predictions thus validating our computational methods.

Original languageEnglish (US)
Pages (from-to)5699-5707
Number of pages9
JournalNucleic Acids Research
Volume43
Issue number12
DOIs
StatePublished - 2015

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ASJC Scopus subject areas

  • Genetics

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