Investigating the Intramolecular Competition of Different RNA Binding Motifs for Neomycin B by Native Top-Down Mass Spectrometry.
FT-ICR
RNA
interactions
mass spectrometry
small molecules
Journal
ChemPlusChem
ISSN: 2192-6506
Titre abrégé: Chempluschem
Pays: Germany
ID NLM: 101580948
Informations de publication
Date de publication:
17 May 2024
17 May 2024
Historique:
revised:
13
04
2024
received:
06
03
2024
medline:
17
5
2024
pubmed:
17
5
2024
entrez:
17
5
2024
Statut:
aheadofprint
Résumé
The ongoing search for small molecule drugs that target ribonucleic acids (RNA) is complicated by a limited understanding of the principles that govern RNA-small molecule interactions. Here we have used stoichiometry-resolved native top-down mass spectrometry (MS) to study the binding of neomycin B to small model hairpin RNAs, an unstructured RNA, and a viral RNA construct. For 15-22 nt model RNAs with hairpin structure, we found that neomycin B binding to hairpin loops relies on interactions with both the nucleobases and the 2'-OH groups, and that a simple 5' or 3' overhang can introduce an additional binding motif. For a 47 nt RNA construct derived from stem IA of the human immunodeficiency virus 1 (HIV-1) rev response element (RRE) RNA, native top-down MS identified four different binding motifs, of which the purine-rich internal loop showed the highest affinity for neomycin B. Stoichiometry-resolved binding site mapping by native top-down MS allows for a new perspective on binding specificity, and has the potential to reveal unexpected principles of small molecule binding to RNA.
Identifiants
pubmed: 38758051
doi: 10.1002/cplu.202400178
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e202400178Subventions
Organisme : Austrian Science Fund
ID : grant DOI 10.55776/P36011
Informations de copyright
© 2024 The Authors. ChemPlusChem published by Wiley-VCH GmbH.
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