Evidence map›Paper›PMID 40884404›Full record

ArticleNucleic acids research2025

High-throughput competitive binding assay for targeting RNA tertiary structures with small molecules: application to pseudoknots and G-quadruplexes.

Sophie E L Wintermans, Jana S Hoffmann, Victor van Kuijk, Yelda Durmus, Mariska D Tacoma, Indy Broekhuizen, Antonius P A Janssen, Hans van den Elst, Bjorn R van Doodewaerd, Paul P Geurink and 2 more

Abstract read
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In one paragraph

Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Sophie E L WintermansDepartment of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.ORCID 0009-0004-7955-6788
Jana S HoffmannDepartment of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.ORCID 0009-0003-0619-9153
Victor van KuijkDepartment of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
Yelda DurmusDepartment of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
Mariska D TacomaDepartment of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
Indy BroekhuizenDepartment of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.ORCID 0009-0004-9629-0037
Antonius P A JanssenDepartment of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden,The Netherlands.ORCID 0000-0003-4203-261X
Hans van den ElstDepartment of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.
Bjorn R van DoodewaerdDepartment of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands.
Paul P GeurinkDepartment of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands.ORCID 0000-0003-1849-1111
Marta ArtolaDepartment of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.ORCID 0000-0002-3051-3902
René C L OlsthoornDepartment of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.ORCID 0000-0003-0315-3005

Funding

Leiden Institute of ChemistryLeiden University
6 · The paper itself

Abstract

There is an indisputable need for new screening methodologies to identify small molecules that target RNA tertiary structures, such as pseudoknots or G-quadruplexes. Here, we present a high-throughput competitive binding antisense assay designed to identify ligands for complex RNA tertiary structures. In this assay, initially customized for the bacterial PreQ1-I riboswitch pseudoknot, ligands compete with a rationally designed quencher-labelled antisense oligonucleotide for binding to a fluorophore-labelled riboswitch. The method is validated for four PreQ1-I riboswitches, using the natural riboswitch ligand PreQ1 and various analogues. A commercial RNA-focused library consisting of ∼15 000 compounds was then screened against the Fusobacterium nucleatum riboswitch, leading to the identification of a promising hit, 4494, which showed competitive binding activity to all PreQ1-I riboswitches and was able to inhibit translation of a riboswitch-regulated reporter gene. Although resynthesis of 4494 revealed that its activity originated from an ∼1% guanine contamination, this result underscores the assay's exceptional sensitivity. To demonstrate its versatility, the assay was tailored for a SARS-CoV-2 G-quadruplex structure and validated with several known G-quadruplex ligands. This work shows that the competitive binding antisense assay is a powerful addition to the RNA-targeting toolbox, facilitating the discovery of ligands for diverse RNA tertiary structures.

Indexed as

G-QuadruplexesHigh-Throughput Screening AssaysRiboswitchSmall Molecule LibrariesBinding, CompetitiveFusobacterium nucleatumHumansLigandsNucleic Acid ConformationOligonucleotides, AntisenseRNARNA, BacterialSARS-CoV-2LigandsOligonucleotides, AntisenseRiboswitchRNARNA, BacterialSmall Molecule Libraries

Identifiers

PMID40884404
PMCPMC12397912

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LicenceCC BY-NC
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.