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

Naoto Hori; Natalia A. Denesyuk; D. Thirumalai

(1) In the high force regime, the two stems are fully ruptured and native interactions are absent creating the E state. (2) Below C ≈ 100 mM and f 10 pN (left bottom on the [C, f ] plane), only S1 is intact, and thus, a hairpin conformation is dominant. This is the interme- The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 diate state, I2, identified by Soto et al. who found that S1 remains stable even at salt concentration as less as 20 mM NaCl [31] . (3) Above C 100 mM and f 10 pN (right bottom), both S1 and S2 stems are formed, and the tertiary interactions involving the two loops are at least partly formed, ensuring that the topology of the PK is native-like. At f = 0 and temperature as a perturbation, it has been shown that another intermediate state, I1, exists between I2 and folded states [30, 31] . The I1 state may correspond to conformations in which two stems are fully folded with the entire topology of the native conformation intact, but tertiary interactions between stems and loops are incomplete. Although we have accounted for the presence of such a state in our simulations (see Fig. 2 ), from here on, we do not distinguish between I1 and the completely folded state in the phase diagram since the increases in Q S2 , Q L1 and Q L2 on the [C, f ] plane almost overlap. Therefore, we classify the right bottom region in the [C, f ] phase diagram as (I1 + F) state.