User:ElNando888/Self-interacting sequences: Difference between revisions

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<tr>
<tr>
<td>Sequence</td>
<td>Sequence</td>
<td><code>CGUCCCGCUUGUCGAGCCCUGGGAGGCUCUGGCGCUGUUCCCAGACAGCUGUCCCAUGGAAUG</code></td>
<td><code>{{ntC}}{{ntG}}{{ntU}}{{ntC}}{{ntC}}{{ntC}}{{ntG}}{{ntC}}{{ntU}}{{ntU}}{{ntG}}{{ntU}}{{ntC}}{{ntG}}{{ntA}}{{ntG}}{{ntC}}{{ntC}}{{ntC}}{{ntU}}{{ntG}}{{ntG}}{{ntG}}{{ntA}}{{ntG}}{{ntG}}{{ntC}}{{ntU}}{{ntC}}{{ntU}}{{ntG}}{{ntG}}{{ntC}}{{ntG}}{{ntC}}{{ntU}}{{ntG}}{{ntU}}{{ntU}}{{ntC}}{{ntC}}{{ntC}}{{ntA}}{{ntG}}{{ntA}}{{ntC}}{{ntA}}{{ntG}}{{ntC}}{{ntU}}{{ntG}}{{ntU}}{{ntC}}{{ntC}}{{ntC}}{{ntA}}{{ntU}}{{ntG}}{{ntG}}{{ntA}}{{ntA}}{{ntU}}{{ntG}}</code></td>
</tr>
</tr>
<tr>
<tr>
<td>MFE<br />(Vienna 2.1.1)&nbsp;</td>
<td>MFE<br />(Vienna 2.1.1)&nbsp;</td>
<td><code>......((((...))))(((((((((((((((........)))))..))).))))).))....</code></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>
<tr>
<tr>
<td>Constrained folding</td>
<td>Constrained folding</td>
<td><code>..........((((((((......))))).)))(((((......)))))..(((...)))...</code></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>
</tbody>
</tbody>

Revision as of 08:13, 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*

PDB accession 1KIS.

 

== 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 .......(((((..((((......))))((..((((((......))))))..))..)))))..

 

Pseudo-switch.png

 

Coaxial stacking predicted for the constrained form:

<tbody> </tbody>
Pseudo-switch1-coax1.png Pseudo-switch1-coax2.png

 

 

=== Candidate 2 ===

<tbody> </tbody>
Sequence AUGCUUCCCCUGGGAGCCCUGGGAGGCUCACAGGCUGUUCCCAGACAGCACGGCAAAUAAGGU
MFE
(Vienna 2.1.1) 
.((((....((((((((((((.........))))..))))))))..)))).............
Constrained folding .((((....(((.(((((......))))).)))(((((......)))))..))))........

 

Pseudo-switch2.png

 

=== Candidate 3 ===

<tbody> </tbody>
Sequence AGUAAUCGAAUAUGAGCCCUGGGAGGCUCUGUUGCUGUUCCCAGACAGCGUCCCUGGCUCUAG
MFE
(Vienna 2.1.1) 
.............(((((..((((.((((((..........))))..)).)))).)))))...
Constrained folding ........((((.(((((......)))))))))(((((......)))))..............

 

Pseudo-switch3.png

 

=== Candidate 4 ===

<tbody> </tbody>
Sequence GCGAAGGGAUAAUGAGCCCUGGGAGGCUCCUUGGCUGUUCCCAGACAGCAAAAUGAGUAUUUU
MFE
(Vienna 2.1.1) 
((...((((.....((((..((((...)))).))))..)))).....))..............
Constrained folding .........(((.(((((......))))).)))(((((......)))))..............

 

Pseudo-switch4.png

 

=== Candidate 5 ===

<tbody> </tbody>
Sequence CGUCCCGCUUGUCGAGCCCUGGGAGGCUCUGGCGCUGUUCCCAGACAGCUGUCCCAUGGAAUG
MFE
(Vienna 2.1.1) 
......((((...))))(((((((((((((((........)))))..))).))))).))....
Constrained folding ..........((((((((......))))).)))(((((......)))))..(((...)))...

 

Pseudo-switch5.png