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_25
Snippet: We did not find any condition in which S1 and S2 are completely folded, but there are no tertiary interactions, U L HB ≈ 0 (i.e., isolated I1 state). Our simulations show that the tertiary interactions contribute to the loop energy only after the stems are formed. Thus, the actual population is distributed between I1 and F, and the tertiary interactions are only marginally stable in the conditions examined here. Soto et al. suggested that diffu.....
Document: We did not find any condition in which S1 and S2 are completely folded, but there are no tertiary interactions, U L HB ≈ 0 (i.e., isolated I1 state). Our simulations show that the tertiary interactions contribute to the loop energy only after the stems are formed. Thus, the actual population is distributed between I1 and F, and the tertiary interactions are only marginally stable in the conditions examined here. Soto et al. suggested that diffuse Mg 2+ ions play an important role in stabilizing such tertiary interactions [31] . Because Mg 2+ is not considered here, we cannot determine the precise interactions stabilizing the I1 state, especially at f = 0. In the discussion hereafter, for simplicity, we refer to (I1 + F) state as F.
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