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

Naoto Hori; Natalia A. Denesyuk; D. Thirumalai

Parsing the U HB due to contributions from interactions among S1, S2, L1, and L2 produces a picture of thermodynamic ordering as C (f ) is increased (decreased) from low (high) value to high (low) value. Low C and high f correspond to the top left region in the phase diagrams (Figs. 4 and 6) . In all conditions, S1 is the first to form as indicated by the presence of distinct peaks at C > 100 mM and f 10 pN in Fig. S5A . Under more favorable conditions (f < 10 pN; C ≈ 300 mM or greater) S2 and tertiary interactions involving L1 are established (Figs. S5 B and C). Only at the highest value of C and f 5 pN, tertiary interactions involving L2 emerge. Interestingly, the order of formation of the various structural elements en route to the formation of their folded state follows the stabilities of the individual elements with the most stable motif forming first. The PK tertiary interactions are consolidated only after the assembly of the stable structural elements. This finding follows from our earlier work establishing that the hierarchical assembly of RNA PKs is determined by the stabilities of individual structural elements [38] .