What are Loops?

A loop is a series of unpaired bases between pairs. (See image: The structure with unpaired bases shown in the yellow rectangle is the loop)

Loops make RNA unstable and prevent RNA from forming stacks. (See image: The structure with adjacent pair bases the green rectangle is the stack)

Usually, longer loops make RNA more unstable. (RNA structure should have shorter loops.)

There are certain sequences that form “loops” that are highly structured and therefore relatively stable, in fact they can be comparable in stability to some helical regions of similar size. These loops are structured by “non-Watson-Crick” basepairs, base-phosphate interactions, and stacking of bases. For examples of loops see the RNA Motif Atlas at:
http://rna.bgsu.edu/rna3dhub/motifs

There are certain sequences that form “loops” that are highly structured and therefore relatively stable, in fact they can be comparable in stability to some helical regions of similar size. These loops are structured by “non-Watson-Crick” basepairs, base-phosphate interactions, and stacking of bases. For examples of loops see the RNA Motif Atlas at:
http://rna.bgsu.edu/rna3dhub/motifs