User:ElNando888/Self-interacting sequences
(work in progress)
== The idea ==
In the future, EteRNA players will face the challenge of creating RNA sequences that can change shape by binding other RNAs rather than reacting to ligands like FMN or Theophylline.
A well-known interaction, HIV TAR-TAR*
== The goal ==
Attempt to find out under which conditions, the hairpins form can be more stable than the MFE, and attempt to quantify the associated kcal bonus.
== Parameters for candidates ==
"Natural" folding (MFE) should
- not have the hairpin features
- not have the complementary hairpin sequences bound together
Constrained folding should
- have the hairpin features
- have as few free bases as possible in the portion inbetween (in an attempt to guarantee that the stems will coaxially stack, thereby nullifying risks of pseudoknot formation)
== Examples ==
=== Candidate 1 ===
<tbody> </tbody>| Sequence | AAACAGUUGGCUUGAGCCCUGGGAGGCUCUGAGGCUGUUCCCAGACAGCUGAGGGUGGCCAUC |
| MFE (Vienna 2.1.1) |
.......(((((...(((((.((..(.((((.((.....)))))))..)).)))))))))).. |
| Constrained folding | .......(((((..((((......))))((..((((((......))))))..))..))))).. |
Coaxial stacking predicted for the constrained form:
<tbody> </tbody> |
 |
=== Candidate 2 ===
<tbody> </tbody>| Sequence | AUGCUUCCCCUGGGAGCCCUGGGAGGCUCACAGGCUGUUCCCAGACAGCACGGCAAAUAAGGU |
| MFE (Vienna 2.1.1) |
.((((....((((((((((((.........))))..))))))))..))))............. |
| Constrained folding | .((((....(((.(((((......))))).)))(((((......)))))..))))........ |
=== Candidate 3 ===
<tbody> </tbody>| Sequence | AGUAAUCGAAUAUGAGCCCUGGGAGGCUCUGUUGCUGUUCCCAGACAGCGUCCCUGGCUCUAG |
| MFE (Vienna 2.1.1) |
.............(((((..((((.((((((..........))))..)).)))).)))))... |
| Constrained folding | ........((((.(((((......)))))))))(((((......))))).............. |
=== Candidate 4 ===
<tbody> </tbody>| Sequence | GCGAAGGGAUAAUGAGCCCUGGGAGGCUCCUUGGCUGUUCCCAGACAGCAAAAUGAGUAUUUU |
| MFE (Vienna 2.1.1) |
((...((((.....((((..((((...)))).))))..)))).....)).............. |
| Constrained folding | .........(((.(((((......))))).)))(((((......))))).............. |
=== Candidate 5 ===
<tbody> </tbody>| Sequence | CGUCCCGCUUGUCGAGCCCUGGGAGGCUCUGGCGCUGUUCCCAGACAGCUGUCCCAUGGAAUG |
| MFE (Vienna 2.1.1) |
......((((...))))(((((((((((((((........)))))..))).))))).)).... |
| Constrained folding | ..........((((((((......))))).)))(((((......)))))..(((...)))... |
Coaxial stacking predicted for the constrained form:
 |
 |
=== Candidate 6 ===
| Sequence | UUAAGAACCGAGGGAGCCCUGGGAGGCUCGGUCUGCUGUUCCCAGACAGCCGUAGAAAGAAAC |
| MFE (Vienna 2.1.1) |
.......((.(((....))).))...(((((.((((((....))).)))))).))........ |
| Constrained folding | ...(((.((....(((((......))))))))))(((((......)))))............. |
Coaxial stacking is not predicted to occur, but the hairpins (marked in white) seem to be predicted to stay distant from each other.
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