Is there any guidance on melting point and its interaction with free energy? I note dimension9’s comments on Improved Statistics Display in Lab Graphics (wherein these
were discussed as added tools):
From Recent RNA Labs
Temp Melt -> Free Energy Range
107C -30 -> -87.8 kC
97C -27.9 -> -46.6 kC
77C -13 -> -28.6 kC
67C -9.8 -> -28.2
57C -10.4 -> -12.5
Anyway, still confused and wondering how to usefully employ melting point in addition
to free energy- much appreciated
Chris,
There isn’t any clear relation between melting point & free energy although generally the lower the free energy, the higher the melting point.
Melting point simply means when the RNA will “unfold” when we increase temperature - generally, higher melting point would mean a more stable RNA and thus a more likely to be successful in lab. This shouldn’t be a deciding factor however, since the model we use for calculating melting point is not perfect.
Melting temperature is defined as the temperature at which 50% of the molecules will be folded and 50% will be unfolded. Well below the Tm, most everything should be folded, and well above, it should be unfolded. Near the Tm, however, you get a transition region where the population is changing rapidly. How wide the transition region is depends on the delta G between the folded and unfolded state (= free energy). A very negative delta G implies a much sharper transition than a puny delta G. For a good discussion of how the two quantities relate to each other, see: