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Internal-loops in RNA are found where the double stranded RNA separates due to no Watson-Crick-Franklin base pairing between the nucleotides. Internal-loops differ from Stem-loops as they occur in middle of a stretch of double stranded RNA. The non-canonicoal residues result in the double helix becoming distorted due to unwinding, unstacking and kinking.
Internal-loops can be classified as either symmetrical or asymmetrical, with some asymmetrical internal-loops, also known as bulges. Many important structural motifs are composed of internal loops such as the C-loop,the docking-elbow,kink-turns ,the right-angle,the sarcin/ricin loops ,the twist-up motifand the UAA/GAN internal loop motif.
A consensus secondary structure and primary sequence for the C-loop RNA motif.
A consensus secondary structure and primary sequence for the docking elbow RNA motif.