Special sequences

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Certain structures in EteRNA can only be solved using one or a few sequences.

 

Contents

Zigzags

Main article: Zigzag

Zigzags have a large number of solutions, but they are not always immediately apparent and are unlikely to be found by random chance.

 

Tricks Involving External Loops

The external loop can be thought of as a multiloop that lacks the quirks of the 3-branched multiloop.

 

1-nt Bulge

The 1-nt bulge attached to an external loop requires one GC pair in the orientation shown. Whe the unpaired base is on the 3' side of the bulge, as shown at right, the GU pair and unpaired U are required. When the unpaired base is on the 5' side of the bulge, an AU or GU pair will suffice.
SpecialSeq1.jpg

 

2-1 Loop

The 2-1 loop attached to an external loop or multiloop is best solved by the UU/U mismatch, but it can be done with a GG/A mismatch. It requires a GC solitary pair.

aa

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