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Open Access Green as soon as Postprint is submitted to ZB.
Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments.
J. Chem. Theory Comput. 19, 3672-3685 (2023)
Chemical probing experiments such as SHAPE are routinely used to probe RNA molecules. In this work, we use atomistic molecular dynamics simulations to test the hypothesis that binding of RNA with SHAPE reagents is affected by cooperative effects leading to an observed reactivity that is dependent on the reagent concentration. We develop a general technique that enables the calculation of the affinity for arbitrary molecules as a function of their concentration in the grand-canonical ensemble. Our simulations of an RNA structural motif suggest that, at the concentration typically used in SHAPE experiments, cooperative binding would lead to a measurable concentration-dependent reactivity. We also provide a qualitative validation of this statement by analyzing a new set of experiments collected at different reagent concentrations.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Selective 2'-hydroxyl Acylation; Nucleic-acids; Force-field; Shape; Secondary; Conformation; Riboswitch; Stability; Accuracy; Reagent
ISSN (print) / ISBN
1549-9618
e-ISSN
1549-9626
Quellenangaben
Volume: 19,
Issue: 12,
Pages: 3672-3685
Publisher
American Chemical Society (ACS)
Publishing Place
Washington, DC
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Structural Biology (STB)