RNA Folding
Unlike DNA, RNA is usually single-stranded, so it folds back on itself: A pairs with U, G with C, and G with U more weakly. Stretches of paired bases form stems, and the unpaired stretches between them form loops. This secondary structure underlies how tRNA carries amino acids, how ribozymes catalyse reactions and how many mRNAs control their own translation.
( pairs with the matching ) and . is unpaired. (((...))) is a hairpin: three bases pair with the last three and enclose a three-base loop.Minimum free energy
A strand can fold in many ways. The thermodynamic approach looks for the structure with the lowest free energy, the minimum free energy (MFE) structure, because that is the most stable. Each stem stacks favourably, each loop costs energy, and the sum is reported in kcal/mol: the more negative, the more stable. The measured values come from the Turner parameters and the search uses Zuker's algorithm.
The simpler method
The Nussinov algorithm only maximises the number of base pairs. It is quick and good for teaching the idea, but it has no energy model, so it ignores that some pairs are much more stable than others. It can disagree considerably with real thermodynamic structures.
How Aaron's Archive does it
| Item | What the tool does |
|---|---|
| Engine | ViennaRNA (the reference implementation of MFE folding) when installed on the server, which is the normal case. Otherwise a clearly labelled Nussinov fallback is used and no energy is shown. |
| Limits | Up to 2,500 nt with ViennaRNA (the algorithm takes cubic time, so long sequences are slow) and 400 nt with the fallback. Longer input is refused with a message, never silently shortened. |
| Output | The dot-bracket structure written under the sequence and its minimum free energy in kcal/mol. |
How far to trust it
An MFE structure is a prediction of the single most stable fold. A real RNA may sit in several shapes at once, fold as it is made, be changed by proteins or ions, or be a different suboptimal structure. Accuracy falls as sequences get longer. Treat the result as a model to test, for instance with chemical probing, not as proof.
Common questions about RNA folding
What is minimum free energy (MFE)?
The folding with the lowest free energy, meaning the most stable base pairing the algorithm can find. The real molecule may fold into a slightly different structure or flip between several.
What is dot-bracket notation?
A line of text that shows the structure: matching brackets are paired bases and dots are unpaired bases.
Why can a prediction be wrong?
The standard algorithm ignores pseudoknots and does not know about proteins, ions or the cell around the RNA, all of which change folding in practice.
How long a sequence can I fold?
Up to 2,500 nucleotides, because the algorithm's running time grows with the cube of the length. Paste an RNA sequence in the Single tab of the tools.