RNA-based Capture-SELEX for the selection of small molecule-binding aptamers

Adrien Boussebayle; Florian Groher; Beatrix Suess

doi:10.1016/j.ymeth.2019.04.004

RNA-based Capture-SELEX for the selection of small molecule-binding aptamers

Methods. 2019 May 15:161:10-15. doi: 10.1016/j.ymeth.2019.04.004. Epub 2019 Apr 4.

Authors

Adrien Boussebayle¹, Florian Groher¹, Beatrix Suess²

Affiliations

¹ Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
² Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany. Electronic address: bsuess@bio.tu-darmstadt.de.

PMID: 30953759
DOI: 10.1016/j.ymeth.2019.04.004

Abstract

Despite their wide applicability, the selection of small molecule-binding RNA aptamers with both high affinity binding and specificity is still challenging. Aptamers that excel at both binding and structure switching are particularly rare and difficult to find. Here, we present the protocol of a Capture-SELEX that specifically allows the in vitro selection of small-molecule binding aptamers, which are essential building blocks for the design process of synthetic riboswitches and biosensors. Moreover, we provide a comparative overview of our proposed methodology versus alternative in vitro selection protocols with a special focus on the design of the pool. Finally, we have included detailed notes to point out useful tips and pitfalls for future application.

Keywords: Aptamer; Capture-SELEX; Riboswitch; SELEX; Synthetic biology.

MeSH terms

Aptamers, Nucleotide / genetics*
Aptamers, Nucleotide / metabolism*
Protein Binding
RNA / genetics*
RNA / metabolism*
Reverse Transcriptase Polymerase Chain Reaction / methods
Reverse Transcription / physiology
SELEX Aptamer Technique / methods*

Substances

Aptamers, Nucleotide
RNA