Urea-Induced Denaturation of PreQ<sub>1</sub>‑Riboswitch
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Abstract
Urea, a polar molecule with a large
dipole moment, not only destabilizes
folded RNA structures but can also enhance the folding rates of large
ribozymes. Unlike the mechanism of urea-induced unfolding of proteins,
which is well understood, the action of urea on RNA has barely been
explored. We performed extensive all-atom molecular dynamics simulations
to determine the molecular underpinnings of urea-induced RNA denaturation.
Urea displays its denaturing power in both secondary and tertiary
motifs of the riboswitch structure. Our simulations reveal that the
denaturation of RNA structures is mainly driven by the hydrogen-bonding
and stacking interactions of urea with the bases. Through detailed
studies of the simulation trajectories, we found that geminate pairs
between urea and bases due to hydrogen bonds and stacks persist only
∼0.1–1 ns, which suggests that the urea–base
interaction is highly dynamic. Most importantly, the early stage of
base-pair disruption is triggered by penetration of water molecules
into the hydrophobic domain between the RNA bases. The infiltration
of water into the narrow space between base pairs is critical in increasing
the accessibility of urea to transiently disrupted bases, thus allowing
urea to displace inter-base hydrogen bonds. This mechanismwater-induced
disruption of base pairs resulting in the formation of a “wet”
destabilized RNA followed by solvation by ureais the exact
opposite of the two-stage denaturation of proteins by urea. In the
latter case, initial urea penetration creates a dry globule, which
is subsequently solvated by water, leading to global protein unfolding.
Our work shows that the ability to interact with both water and polar
or nonpolar components of nucleotides makes urea a powerful chemical
denaturant for nucleic acids