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

Naoto Hori; Natalia A. Denesyuk; D. Thirumalai

The slope of the f c versus log C m is proportional to the changes in the preferential interaction coefficient between an intermediate and unfolded states. This prediction can be used in conjunction with single-molecule experiments allowing for direct measurement of a key quantity in ion-RNA interactions; and (3) To the extent the downstream PK is a roadblock for translation, our work suggests that the ribosome should exert a force ∼ (10 − 15) pN [36] for unimpeded translocation along mRNA, although the actual force value could vary depending on factors such as interaction between PK and ribosome. Based in part on our work we propose that there should be a link between the stimulatory effect of frameshifting and the stability of the 5 -end of the PK. Our predictions are amenable to validations using single-molecule experiments.