Secondary Structural Motifs in RNA

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The secondary structure of RNA contains several types of recurring features. These are often referred to as secondary structural elements.


Stacks are base paired regions of RNA. Stacks are generally stabilizing; they make a negative contribution to free energy. A stack on flanked on either side by loops is an "isolated" or "lonely" base pair. Isolated base pairs can be conceptualized as stack one base pair in length.


A loop is a region of RNA that contains at least one unpaired base. Loops are further categorized based on the number of adjoining stacks and their location within the RNA molecule. Loops may be stabilizing or destabilizing depending on their size, sequence, and type.

Hairpin Loops

Main Article: Hairpin Loop

Hairpins are formed when a stretch of RNA folds back on itself to create a stack and a single-stranded loop. Hairpin loops are joined to only one stack. Together, this stack and the hairpin are known as a stem-loop structure. Hairpin loops can be boosted.

Internal Loops

Main Article: Internal Loop

Internal loops are formed when mismatched bases occur across from one another in a stack. An internal loop is named according to the number of mismatched bases on either side of the stack. Internal loops can be boosted.


Main Article: Bulge

Bulges are a special type of internal loop where only one strand contains unpaired bases. Bulges cannot be boosted.


Main article: Multiloop

Multiloops, or multi-branched loops, are loops that are joined to three or more stacks. Certain multiloops can be boosted.

External Loops

Main Article: External Loop

External loops contain one or more base pairs as well as the 3' and 5' termini of the RNA molecule. The termini are also known as "dangling ends". Certain external loops can be boosted.