The minimum free energy of an RNA secondary structure is generally said to correspond to the energy lost due to nucleotide base pairing. Therefore I cannot see the difference between two sequences with the 5' and 3' ends replaced.
Can anyone explain why we get a different MFE (and MFE structure) when we replace the two termini i.e. present the original sequence in reversed order?
@jJan.What you call minimum free energy is just a rough caricature (bioinformatician' s world) of the true free energy of RNA in water +ions+.etc. which considers via another caricature (of H-bonding) the matching of complementary stretches of the sequence.It is a useful caricature for some purposes,but cannot depend on directionality.However if you progressively make the caricature better by approximately, including base stacking and structural waters you will find that the MFE and minimizing structure depends on directionality and that the minimal structure may locally have both antiparallel and parallel complimentary strands.(with reverse Watson-Crick or Hoogsten pairing).Unfortunately, he biophysicist's world is more complex than that of
in silico RNA folders.
one more thing: G:U are a valid pair while the reverse complementary A:C are not.
Hi again,
In fact, the minimum free energy structure predicted by bioinformatics tools does depend on directionality (just try it out, for example using RNAfold). I know that the prediction relies on the partition function and that different nucleotides may have different energetic contributions but I still don't understand why the outcome MFE structures are different.
Jan
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