 RNA melting temperature

ID: rna-melting-temperature

An RNA melting temperature,

T_{m}

, characterizes the midpoint of a specified RNA conformational transition under stated conditions. In a reversible, unimolecular two-state RNA melting model, it is the temperature at which folded and unfolded populations are equal. A midpoint assigned to an optical trace requires a model connecting absorbance to those populations.

Let unfolding free energy be

Δ G_{u} = G_{U} - G_{F}

. If unfolding enthalpy and entropy are treated as temperature independent,

Δ G_{u} (T) = Δ H_{u} - T Δ S_{u}, T_{m} = \frac{Δ H _{u}}{Δ S _{u}} .

The formula assumes a finite relevant transition and uses absolute temperature. With original stipulated values

Δ H_{u} = 100 kJ mo l^{- 1}

and

Δ S_{u} = 300 J mo l^{- 1} K^{- 1}

T_{m} \approx 333.3 K

. Holding enthalpy fixed but changing entropy to

310 J mo l^{- 1} K^{- 1}

gives approximately

322.6 K

. A melting temperature reflects both energetic and entropic contributions.

Molecularity matters. An ideal intramolecular hairpin transition need not change its midpoint with total strand concentration. A transition involving association of separate strands generally does: the equilibrium relation includes their concentrations. The concentration dependence of RNA melting can therefore help test which structural model is appropriate. In the 2010 tetraloop measurements, concentration-independent curves across a broad concentration range supported stem–loop formation.^[ref]

A raw halfway absorbance is not automatically this thermodynamic midpoint. If the folded and unfolded RNA melting baselines at one temperature are

0.55

and

0.75

0.60

implies unfolded fraction

0.25

, not

0.50

. Intermediates, temperature-dependent parameters or RNA melting hysteresis can further complicate midpoint assignment. Report the solution conditions and definition of the measured transition rather than treating

T_{m}

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