Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension

Naoto Hori; Natalia A. Denesyuk; D. Thirumalai

From the coefficients in the dependence of f c on log C m , we can estimate ∆Γ which provides a quantitative estimation of the extent of ion-RNA interactions [45] . For the E I transition, ∆R ee ≈ 4.9 nm and the slope of the linear function is 1.7 pN, which leads to ∆Γ EI = 0.96 (Fig. 8C ). This indicates that upon the conformational change from unfolded to the intermediate state, one ion pair enters the atmosphere of the PK. For the transition between I and F, fitting the dependence of ∆R IF ee on f IF c with a = 0.14 nm/pN and b = 0.27 nm (Fig. 9C) , we estimate ∆Γ IF = 1.8 using Eq.(6) (Fig. 8D) . Consequently, the total number of excess cations effectively bound to folded RNA is expected to be around 2.8, a value that is in rough accord with the experimental estimate of 2.2 [30] . More importantly, ∆Γ αβ can be measured using LOT and magnetic tweezer experiments [39] [40] [41] [42] [43] , thus expanding the scope of such experiments to measure ion-RNA interactions. A recent illustration of the efficacy of single-molecule experiments is the study by Jacobson and Saleh who quantified ∆Γ from force measurements for an RNA hairpin [43] .