Dissertation

A competitive binding assay for RNA ligand discovery

In the emerging field of small-molecule RNA targeting, there is a growing demand for new high-throughput screening methods.

Author: S.E.L. Wintermans
Date: 24 February 2026
Links: Thesis in Leiden Repository

This thesis describes the development of a competitive binding antisense assay (CB ASsay), in which small molecules compete with a specifically designed antisense oligonucleotide to bind to the target RNA. This allows for the identification of new RNA ligands for clinically relevant RNA tertiary structures. The CB ASsay was employed to three pathogenic RNA targets: the bacterial PreQ₁ riboswitch, the SARS-CoV-2 frameshifting pseudoknot and the G-quadruplex at position 3467 in the SARS-CoV-2 genome (GQ-3467). The CB ASsay is highly sensitive, applicable to various RNA structures and is particularly well-suited for high-throughput screenings. Screening the Enamine RNA-focused library and the European Lead Factory library led to the identification of several hit molecules that can now be investigated for their antimicrobial properties. All in all, this thesis demonstrates that the CB ASsay is an important addition to the RNA-targeting toolbox.