One of the key factors in -1 programmed ribosomal frameshifting (PRF) is a pseudoknot (PK) RNA . A number of single molecule  experiments have been performed on PKs to decipher the mechanism of PRF. Motivated by the experiments, we performed simulations  to describe the response of a PK over a range of mechanical forces (fs) and monovalent salt concentrations (Cs). The coarse-grained simulations quantitatively reproduces the multistep thermal melting  . The free energy changes obtained in simulations are in excellent agreement with experiments , thus validating our model. The predicted phase diagram shows that a sequence of structural transitions, populating distinct intermediates, occur as f and C are changed . The stem-loop tertiary interactions rupture first followed by unfolding of the 3^{\prime}-end hairpin (\textrm{ U-I } \textrm{ ). Finally, the 5^{\prime}-end hairpin unravels producing a stretched state ( \textrm{ I-F } \textrm{ ). A theoretical analysis of the phase boundaries shows that the critical force for rupture scales as \left(\log C_{\textrm{m}}\right)^{\alpha} with \alpha=1\,(0.5) for \textrm{ U-I ( \textrm{  \textrm{ I-F } \textrm{ ) transition. This relation is used to obtain the ion-preferential coefficients, which shows that ion-RNA interactions can be quantitatively measured in single molecule experiments . Our simulations predict a plausible link between the stability of the 5^{\prime} hairpin and efficiency of PRF .
Because of the potential link between -1 programmed ribosomal frameshifting (PRF) and response of a pseudoknot (PK) RNA to force, a number of single molecule pulling experiments have been performed on PKs to decipher the mechanism of PRF. Motivated in part by these experiments, we performed simulations using a coarse-grained model of RNA to describe the response of a PK over a range of mechanical forces (fs) and monovalent salt concentrations (Cs). The coarse-grained simulations quantitatively reproduce the multistep thermal melting observed in experiments, thus validating our model . The free energy changes obtained in simulations are in excellent agreement with experiments . By varying f and C, we calculated the phase diagram that shows a sequence of structural transitions, populating distinct intermediate states. As f and C are changed , the stem-loop tertiary interactions rupture first followed by unfolding of the 3^{\prime}-end hairpin (\textrm{ I } \rightleftharpoons\textrm{F ). Finally, the 5^{\prime}-end hairpin unravels producing a extended state ( \textrm{ E } \rightleftharpoons\textrm{I ). A theoretical analysis of the phase boundaries shows that the critical force for rupture scales as \left(\log C_{\textrm{m}}\right)^{\alpha} with \alpha=1\,(0.5) for \textrm{ E \rightleftharpoons\textrm{I ( \textrm{ I } \rightleftharpoons\textrm{F ) transition. This relation is used to obtain the preferential ion-RNA interaction coefficient, which can be quantitatively measured in single molecule experiments , as done previously for DNA hairpins. A by product of our work is the suggestion that the frameshift efficiency is likely determined by the stability of the 5^{\prime} -end hairpin that the ribosome first encounters during translation .
R
One of the key factors in
Because of the potential link between
R
is
and response of
R
. A
to force, a
A
pulling
R
by the
in part by these
A
using a coarse-grained model of RNA
R
reproduces
reproduce
A
observed in experiments, thus validating our model
R
, thus validating our model. The predicted phase diagram shows that
. By varying f and C, we calculated the phase diagram that shows
R
intermediates, occur as
intermediate states. As
R
. The
, the
R
U-I
I
A
\rightleftharpoons
A
F
R
stretched state (
extended state (
R
I-F
E
A
\rightleftharpoons
A
I
D
U-I
R
(
E
A
\rightleftharpoons
A
I
A
(
R
I-F
I
A
\rightleftharpoons
A
F
R
ion-preferential coefficients, which shows that
preferential
R
interactions
interaction coefficient, which
R
. Our simulations predict a plausible link between the
, as done previously for DNA hairpins. A by product of our work is the suggestion that the frameshift efficiency is likely determined by the
R
hairpin and efficiency of PRF
-end hairpin that the ribosome first encounters during translation