1 research outputs found
Non-specific binding of Na and Mg to RNA determined by force spectroscopy methods
RNA duplex stability depends strongly on ionic conditions, and inside cells
RNAs are exposed to both monovalent and multivalent ions. Despite recent
advances, we do not have general methods to quantitatively account for the
effects of monovalent and multivalent ions on RNA stability, and the
thermodynamic parameters for secondary structure prediction have only been
derived at 1M [Na]. Here, by mechanically unfolding and folding a 20 bp RNA
hairpin using optical tweezers, we study the RNA thermodynamics and kinetics at
different monovalent and mixed monovalent/Mg salt conditions. We measure
the unfolding and folding rupture forces and apply Kramers theory to extract
accurate information about the hairpin free energy landscape under tension at a
wide range of ionic conditions. We obtain non-specific corrections for the free
energy of formation of the RNA hairpin and measure how the distance of the
transition state to the folded state changes with force and ionic strength. We
experimentally validate the Tightly Bound Ion model and obtain values for the
persistence length of ssRNA. Finally, we test the approximate rule by which the
non-specific binding affinity of divalent cations at a given concentration is
equivalent to that of monovalent cations taken at 100 fold that concentration
for small molecular constructs.Comment: main paper (32 pages, 11 figures, 1 table) + supplementary
information (15 pages