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

Naoto Hori; Natalia A. Denesyuk; D. Thirumalai

The simulation results in Fig. 2 and Fig. S1 show that melting of BWYV PK undergoes through two intermediate states, F I1 I2 U where I1 has the topology of the F state but without significant tertiary interactions (Fig. 3) . Although simulations can be used to distinguish I1 and F states, the intermediate does not have significant population. The identification of I1 in our simulations provides a structural support to experiments in which I1 was inferred from three broad overlapping peaks in the heat capacity curves [30, 31] . It should be stressed that the experimental heat capacity curves exhibit only two discernible peaks, which would normally imply that there is only one intermediate present. The range of melting temperatures for the three transitions can be obtained from the temperature dependence of the various states f α (T ) (α=F, I1, I2 or U) given in Fig. 2C . The I1 state has a maximum population around T ≈ 50 • C. We equate this with the melting temperature T m1 associated with the F I1 transition. Similarly, T m2 for the I1 I2 transition is ≈ 70 • C. The T m3 for the I2 U transition occurs around 90 • C (f I2 (T m3 ) = f U (T m3 )). The values of the three melting temperatures obtained in our simulations are in remarkable agreement with experiments (T exp. m1 =59.4 • C, T exp. m2 =69.4 • C, and T exp. m3 =91.2 • C taken from results of a differential scanning calorimetry experiment at pH=7 in Table 1 of Nixon and Giedroc [30] ).