 RNA hairpin melting

RNA hairpin melting is the temperature-dependent loss of the folded stem-loop structure of an RNA hairpin. Here melting describes a molecular conformational transition in solution, rather than conversion of a solid sample into a liquid. Changing temperature shifts the relative populations of folded and unfolded RNA.

In optical measurements, a spectrophotometer tracks absorbance while the RNA solution is heated under controlled conditions. Changes in base stacking can alter ultraviolet absorbance, an effect associated with RNA hyperchromicity. In a 2010 tetraloop study, researchers recorded absorbance-versus-temperature curves, repeated measurements over an approximately 50-fold RNA concentration range, and observed concentration-independent transitions. That behavior supported intramolecular hairpin formation rather than association of separate strands.^[ref]

An explicit two-state model lets F and U denote folded and unfolded RNA. Define unfolding free energy $\Delta G_u=G_U-G_F$ and take temperature-independent unfolding parameters $\Delta H_u$ and $\Delta S_u$:Here $T$ is absolute temperature and $R$ the molar gas constant. The RNA melting temperature satisfies $\Delta G_u(T_m)=0$, hence $T_m=\Delta H_u/\Delta S_u$ and $f_U(T_m)=1/2$ in this model.

For original stipulated values $\Delta H_u=120\mathrm{kJ}\mathrm{mo}{\mathrm{l}}^{-1}$ and $T_m=330\mathrm{K}$, the predicted unfolded fractions at $300$, $330$ and $360\mathrm{K}$ are approximately $0.012$, $0.500$ and $0.975$. They are model calculations, not measurements from the cited study.

Raw absorbance is not automatically the unfolded fraction. Even in a two-state interpretation, folded and unfolded baselines can vary with temperature: $A(T)=[1-f_U(T)]A_F(T)+f_U(T)A_U(T)$. Baseline estimates, reversibility and alternative conformations affect the inference. A smooth single transition is useful evidence, but it does not independently prove that every RNA molecule follows one microscopic pathway.