User talk:ElNando888/Self-interacting sequences

 

 

== Documented candidates ==

=== Candidate 1 ===

==== Raw data ====

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Sequence	AAGUGAACUAUGGGAGCCCUGGGAGGCUCCUCCUGCUGUUCCCAGACAGCAAAAGCCUGUUGG
MFE (Vienna 2.1.1)	..........(((((((..((((((....))))))..)))))))..(((((......))))).	-21.7
Fully constrained	..................xxxxxx...............xxxxxx.................. ...........(((((((......)))))))..((((((......))))))............	-19.4
Constraint hairpin 1	..................xxxxxx....................................... ...........(((((((......)))))))..(((((((....)))))))............	-20.5
Constraint hairpin 2	.......................................xxxxxx.................. ...........(((((((......)))))))..((((((......))))))............	-19.4
Hairpins seq. paired	..................((((((...............)))))).................. ..................(((((((((.......)))..)))))).(((((......))))).	-15.8

 

==== 2D and 3D shots ====

(coming soon)

 

==== Comments ====

• The delta between the MFE and the hairpins form is both low (hopefully helping the targeted 'pseudo-switching' behavior) and large enough to make it clear that the experiment failed if the 'pseudo-switching' should not occur at all.
• The formation of either of the hairpins (and its possible kissing complex forming) should result in the other hairpin forming as well.
• The form with the hairpin sequences forming a stack is comparatively unlikely (high kcal delta)

 

 

== Other examples ==

(need re-analysis)

 

=== Candidate 1 ===

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Sequence	AAACAGUUGGCUUGAGCCCUGGGAGGCUCUGAGGCUGUUCCCAGACAGCUGAGGGUGGCCAUC
MFE (Vienna 2.1.1)	.......(((((...(((((.((..(.((((.((.....)))))))..)).))))))))))..
Constrained folding	.......(((((..((((......))))((..((((((......))))))..))..)))))..

 

 

Coaxial stacking predicted for the constrained form:

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=== Candidate 2 ===

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Sequence	AUGCUUCCCCUGGGAGCCCUGGGAGGCUCACAGGCUGUUCCCAGACAGCACGGCAAAUAAGGU
MFE (Vienna 2.1.1)	.((((....((((((((((((.........))))..))))))))..)))).............
Constrained folding	.((((....(((.(((((......))))).)))(((((......)))))..))))........

 

 

=== Candidate 3 ===

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Sequence	AGUAAUCGAAUAUGAGCCCUGGGAGGCUCUGUUGCUGUUCCCAGACAGCGUCCCUGGCUCUAG
MFE (Vienna 2.1.1)	.............(((((..((((.((((((..........))))..)).)))).)))))...
Constrained folding	........((((.(((((......)))))))))(((((......)))))..............

 

 

=== Candidate 4 ===

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Sequence	GCGAAGGGAUAAUGAGCCCUGGGAGGCUCCUUGGCUGUUCCCAGACAGCAAAAUGAGUAUUUU
MFE (Vienna 2.1.1)	((...((((.....((((..((((...)))).))))..)))).....))..............
Constrained folding	.........(((.(((((......))))).)))(((((......)))))..............

 

 

=== Candidate 5 ===

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Sequence	CGUCCCGCUUGUCGAGCCCUGGGAGGCUCUGGCGCUGUUCCCAGACAGCUGUCCCAUGGAAUG
MFE (Vienna 2.1.1)	......((((...))))(((((((((((((((........)))))..))).))))).))....
Constrained folding	..........((((((((......))))).)))(((((......)))))..(((...)))...

 

Coaxial stacking predicted for the constrained form:

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=== Candidate 6 ===

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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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