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BoyscoutRNA

Here you can see the long chain of Uracil and Adenine, forming the classic blue and gold pattern for which this type of designing misstep is named.

"Cub scouts" are lab designs that have an undesirably high percentage of AU pairs. This leads to a high possiblity of the RNA mispairing when folding due to the high availability of A's and U's and their relatively strong attraction to each other. Flipping the bases to help stabilize the stacks will help, but only help to a certain extent in these cases, and the long, unbroken strands of AU may eventually mispair unless the string is quite near a straight line in shape.

This type of RNA often appears when users get too comfortable utilizing the AU bonds or get in a hurry with long strings of RNA. The 'ideal' percentage of AU bonds should be in the ballpark of 25%, and this design clearly goes well beyond that percentage. Cub scout RNAs can be alleviated by converting some of the AU bonds into GU bonds or by occasionally adding GC bonds in the middle of the stacks.

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