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

Naoto Hori; Natalia A. Denesyuk; D. Thirumalai

The considerations given above and the availability of both ensemble and single-molecule pulling experimental data prompted us to focus on the effects of temperature, mechanical force, and salt concentration on a 28nucleotide H-type RNA PK from the beet western yellow virus (BWYV) [19] . This PK has been the subject of several ensemble experiments, which have characterized the folding thermodynamics as a function of monovalent and divalent cations [30, 31] . The BWYV PK has two stems (S1 and S2) connected by two loops (L1 and L2) as shown in Fig. 1 . The crystal structure reveals that L2 forms triplex-type tertiary interactions with S1 [32] . In another context, it has been shown that such interactions and mutations affecting them dramatically change the efficiency of frameshifting [21] . In vitro and in vivo experiments on many mutants of BWYV suggest [32] color-coded according to secondary structures. The black arrows indicate positions at which the external mechanical force is applied. (B) Schematic representation of the secondary structure. Unlike the typical H-type pseudoknot, the two helix stems (S1 and S2) are not coaxially stacked in the BWYV pseudoknot [25] . Tertiary interactions are indicated by red dashed lines.