User:ElNando888/Self-interacting sequences: Difference between revisions
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<p> </p> | <p> </p> | ||
<p>[[File:Pseudo-switch3.png|650px]]</p> | <p>[[File:Pseudo-switch3.png|650px]]</p> | ||
<p> </p> | |||
<p>=== Candidate 4 ===</p> | |||
<table border="0" cellpadding="3"> | |||
<tbody> | |||
<tr> | |||
<td>Sequence</td> | |||
<td><code>{{ntG}}{{ntC}}{{ntG}}{{ntA}}{{ntA}}{{ntG}}{{ntG}}{{ntG}}{{ntA}}{{ntU}}{{ntA}}{{ntA}}{{ntU}}{{ntG}}{{ntA}}{{ntG}}{{ntC}}{{ntC}}{{ntC}}{{ntU}}{{ntG}}{{ntG}}{{ntG}}{{ntA}}{{ntG}}{{ntG}}{{ntC}}{{ntU}}{{ntC}}{{ntC}}{{ntU}}{{ntU}}{{ntG}}{{ntG}}{{ntC}}{{ntU}}{{ntG}}{{ntU}}{{ntU}}{{ntC}}{{ntC}}{{ntC}}{{ntA}}{{ntG}}{{ntA}}{{ntC}}{{ntA}}{{ntG}}{{ntC}}{{ntA}}{{ntA}}{{ntA}}{{ntA}}{{ntU}}{{ntG}}{{ntA}}{{ntG}}{{ntU}}{{ntA}}{{ntU}}{{ntU}}{{ntU}}{{ntU}}</code></td> | |||
</tr> | |||
<tr> | |||
<td>MFE<br />(Vienna 2.1.1) </td> | |||
<td><code>{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|.}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}</code></td> | |||
</tr> | |||
<tr> | |||
<td>Constrained folding</td> | |||
<td><code>{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|(}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|)}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}{{alignNt|.}}</code></td> | |||
</tr> | |||
</tbody> | |||
</table> | |||
<p> </p> | |||
<p>[[File:Pseudo-switch4.png|650px]]</p> | |||
Revision as of 23:55, 26 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 | .......(((((..((((......))))((..((((((......))))))..))..))))).. |
=== 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 | .........(((.(((((......))))).)))(((((......))))).............. |
