User:ElNando888/Self-interacting sequences: Difference between revisions
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<p>In the future, EteRNA players will face the challenge of creating RNA [[sequence]]s that can change shape by binding other [[RNA]]s rather than reacting to [[ligand]]s like [[FMN]] or [[Theophylline]].</p> | <p>In the future, EteRNA players will face the challenge of creating RNA [[sequence]]s that can change shape by binding other [[RNA]]s rather than reacting to [[ligand]]s like [[FMN]] or [[Theophylline]].</p> | ||
<p> </p> | <p> </p> | ||
<p>A well-known interaction HIV TAR-TAR*</p> | <p>A well-known interaction, HIV TAR-TAR*</p> | ||
<p>[http://www.rcsb.org/pdb/explore.do?structureId=1kis PDB accession 1KIS].</p> | <p>[http://www.rcsb.org/pdb/explore.do?structureId=1kis PDB accession 1KIS].</p> | ||
<p> </p> | <p> </p> | ||
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<p> </p> | <p> </p> | ||
<p>[[File:Pseudo-switch.png|650px]]</p> | <p>[[File:Pseudo-switch.png|650px]]</p> | ||
<p> </p> | |||
<p>Coaxial stacking predicted for the constrained form:</p> | |||
<table border="0" cellpadding="3"> | |||
<tbody> | |||
<tr> | |||
<td>[[File:Pseudo-switch1-coax1.png|x400px]]</td> | |||
<td>[[File:Pseudo-switch1-coax2.png|x400px]]</td> | |||
</tr> | |||
</tbody> | |||
</table> | |||
<p> </p> | |||
<p> </p> | <p> </p> | ||
<p>=== Candidate 2 ===</p> | <p>=== Candidate 2 ===</p> | ||
Revision as of 00:45, 27 May 2013
(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 | .........(((.(((((......))))).)))(((((......))))).............. |
