  Riboswitches, RNA elements found in the untranslated region, regulate gene
expression by binding to target metaboloites with exquisite specificity.
Binding of metabolites to the conserved aptamer domain allosterically alters
the conformation in the downstream expression platform. The fate of gene
expression is determined by the changes in the downstream RNA sequence. As the
metabolite-dependent cotranscriptional folding and unfolding dynamics of
riboswitches is the key determinant of gene expression, it is important to
investigate both the thermodynamics and kinetics of riboswitches both in the
presence and absence of metabolite. Single molecule force experiments that
decipher the free energy landscape of riboswitches from their mechanical
responses, theoretical and computational studies have recently shed light on
the distinct mechanism of folding dynamics in different classes of
riboswitches. Here we first discuss the dynamics of water around riboswitch,
highlighting that water dynamics can enhance the fluctuation of nucleic acid
structure. To go beyond native state fluctuations we used the Self-Organized
Polymer (SOP) model to predict the dynamics of add adenine riboswitch under
mechanical forces. In addition to quantitatively predicting the folding
landscape of add-riboswitch our simulations also explain the difference in the
dynamics between pbuE adenine- and add adenine-riboswitches. In order to probe
the function {\it in vivo} we use the folding landscape to propose a system
level kinetic network model to quantitatively predict how gene expression is
regulated for riboswitches that are under kinetic control.
