Salt effect on thermodynamics and kinetics of a single RNA base pair.
RNA base pair
kinetics
salt effect
thermodynamics
Journal
RNA (New York, N.Y.)
ISSN: 1469-9001
Titre abrégé: RNA
Pays: United States
ID NLM: 9509184
Informations de publication
Date de publication:
04 2020
04 2020
Historique:
received:
06
11
2019
accepted:
11
01
2020
pubmed:
29
1
2020
medline:
18
6
2020
entrez:
29
1
2020
Statut:
ppublish
Résumé
Due to the polyanionic nature of RNAs, the structural folding of RNAs are sensitive to solution salt conditions, while there is still lack of a deep understanding of the salt effect on the thermodynamics and kinetics of RNAs at a single base-pair level. In this work, the thermodynamic and the kinetic parameters for the base-pair AU closing/opening at different salt concentrations were calculated by 3-µsec all-atom molecular dynamics (MD) simulations at different temperatures. It was found that for the base-pair formation, the enthalpy change [Formula: see text] is nearly independent of salt concentration, while the entropy change [Formula: see text] exhibits a linear dependence on the logarithm of salt concentration, verifying the empirical assumption based on thermodynamic experiments. Our analyses revealed that such salt concentration dependence of the entropy change mainly results from the dependence of ion translational entropy change for the base pair closing/opening on salt concentration. Furthermore, the closing rate increases with the increasing of salt concentration, while the opening rate is nearly independent of salt concentration. Additionally, our analyses revealed that the free energy surface for describing the base-pair opening and closing dynamics becomes more rugged with the decrease of salt concentration.
Identifiants
pubmed: 31988191
pii: rna.073882.119
doi: 10.1261/rna.073882.119
pmc: PMC7075264
doi:
Substances chimiques
Sodium Chloride
451W47IQ8X
RNA
63231-63-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
470-480Informations de copyright
© 2020 Wang et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
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