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Does an RNA double strand containing the nucleobase T instead of U has a lower free energy?

Or more precisely: There are tabulated values for the change in free energy of the canonical neighboring base pairs here. Do you know of any source where values for neighboring base pairs of e.g. GT/CA got compared to GU/CA?

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  • $\begingroup$ I think you mean bond energies. $\endgroup$
    – David
    Dec 10, 2020 at 16:29
  • $\begingroup$ If you want you can call "free energy of neighboring base pairs" the bond energy. But I think it is less precise. $\endgroup$
    – newandlost
    Dec 11, 2020 at 19:24
  • $\begingroup$ I was under the impression that you could only measure free energy changes, not free energy. And presumably bond energies would be equivalent to the free energy changes in breaking a hydrogen bond. But my chemistry is a little rusty, so do point me to sources that measure actual free energies of base pairs of any sort. $\endgroup$
    – David
    Dec 11, 2020 at 20:16
  • $\begingroup$ Ah no, you are right! It is change in free energy. I adapt my question. $\endgroup$
    – newandlost
    Dec 11, 2020 at 20:23
  • $\begingroup$ I think my problem with bond energy is that the change in free energy is not simply the breakage of hydrogen bonds. It is an interplay between stacking (pi-pi) and hydrogen bonding. $\endgroup$
    – newandlost
    Dec 11, 2020 at 20:29

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