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Calonaci, N.* ; Bernetti, M.* ; Jones, A. ; Sattler, M. ; Bussi, G.*

Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments. 

J. Chem. Theory Comput. 19, 3672-3685 (2023)
DOI PMC
Open Access Green möglich sobald Postprint bei der ZB eingereicht worden ist.
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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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Selective 2'-hydroxyl Acylation; Nucleic-acids; Force-field; Shape; Secondary; Conformation; Riboswitch; Stability; Accuracy; Reagent
ISSN (print) / ISBN 1549-9618
e-ISSN 1549-9626
Zeitschrift Journal of Chemical Theory and Computation
Quellenangaben Band: 19, Heft: 12, Seiten: 3672-3685 Artikelnummer: , Supplement: ,
Verlag American Chemical Society (ACS)
Verlagsort Washington, DC
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Structural Biology (STB)