Author: Naoto Hori; Natalia A. Denesyuk; D. Thirumalai
Title: Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension Document date: 2016_4_15
ID: 08mep8hm_37
Snippet: Our analysis is based on the assumption that ∆Γ is a constant independent of the salt concentration. However, it is known experimentally that ∆Γ deviates from a constant value at high salt concentration [41, 43, 46] . The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/048801 doi: bioRxiv preprint In Fig. 8C and D, theoretical lines (blue dotted) show such a deviation from .....
Document: Our analysis is based on the assumption that ∆Γ is a constant independent of the salt concentration. However, it is known experimentally that ∆Γ deviates from a constant value at high salt concentration [41, 43, 46] . The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/048801 doi: bioRxiv preprint In Fig. 8C and D, theoretical lines (blue dotted) show such a deviation from ∆G = 0 of the simulation data (white region) at high salt concentration (C 500 mM). Therefore, we believe that our theoretical analysis is most accurate for C 500 mM. Our coarse-grained simulation reflects the nonlinearity of ∆Γ observed in previous experiments. Understanding the origin of the nonlinearity requires a microscopic theory that should take into account the effects of ion-ion correlations. For complex architectures such as PK or ribozymes, this does not appear straightforward.
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