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

42 Citations (Scopus)

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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SELEX Aptamer Technique
Interleukin-10 Receptor alpha Subunit
Cluster Analysis
Technology
High-Throughput Nucleotide Sequencing

ASJC Scopus subject areas

  • Genetics

Cite this

Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery. / Hoinka, Jan; Berezhnoy, Alexey; Dao, Phuong; Sauna, Zuben E.; Gilboa, Eli; Przytycka, Teresa M.

In: Nucleic Acids Research, Vol. 43, No. 12, 2015, p. 5699-5707.

Research output: Contribution to journalArticle

Hoinka, J, Berezhnoy, A, Dao, P, Sauna, ZE, Gilboa, E & Przytycka, TM 2015, 'Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery', Nucleic Acids Research, vol. 43, no. 12, pp. 5699-5707. https://doi.org/10.1093/nar/gkv308
Hoinka, Jan ; Berezhnoy, Alexey ; Dao, Phuong ; Sauna, Zuben E. ; Gilboa, Eli ; Przytycka, Teresa M. / Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery. In: Nucleic Acids Research. 2015 ; Vol. 43, No. 12. pp. 5699-5707.
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