Internal loop explained

Internal-loops (also termed interior 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,^[1] the docking-elbow,^[2] kink-turns (k-turn),^{[3] [4]} the right-angle,^[5] the sarcin/ricin loops (also called bulged-G motifs),^{[6] [7] [8]} the twist-up motif^[9] and the UAA/GAN internal loop motif.^[10]

See also

• Stem-loop
• Nucleic acid secondary structure

Notes and References

1. Lescoute. A. Leontis. NB. Massire. C. Westhof. E. Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments.. Nucleic Acids Research. 2005. 33. 8. 2395–409. 15860776. 10.1093/nar/gki535. 1087784.
2. Lehmann. J. Jossinet. F. Gautheret. D. A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders.. Nucleic Acids Research. May 1, 2013. 41. 10. 5494–502. 23580544. 10.1093/nar/gkt219. 3664808.
3. Klein. D.J.. The kink-turn: a new RNA secondary structure motif. The EMBO Journal. 20. 15. 2001. 4214–4221. 1460-2075. 10.1093/emboj/20.15.4214. 149158. 11483524.
4. Schroeder. KT. McPhee. SA. Ouellet. J. Lilley. DM. A structural database for k-turn motifs in RNA.. RNA. Aug 2010. 16. 8. 1463–8. 20562215. 10.1261/rna.2207910. 2905746.
5. Grabow. WW. Zhuang. Z. Swank. ZN. Shea. JE. Jaeger. L. The right angle (RA) motif: a prevalent ribosomal RNA structural pattern found in group I introns.. Journal of Molecular Biology. Nov 23, 2012. 424. 1–2. 54–67. 22999957. 10.1016/j.jmb.2012.09.012. 3488136.
6. Szewczak. AA. Moore. PB. The sarcin/ricin loop, a modular RNA.. Journal of Molecular Biology. Mar 17, 1995. 247. 1. 81–98. 7897662. 10.1006/jmbi.1994.0124. free.
7. Leontis. NB. Westhof. E. A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs.. Journal of Molecular Biology. Oct 30, 1998. 283. 3. 571–83. 9784367. 10.1006/jmbi.1998.2106.
8. Moore PB . Structural motifs in RNA . Annu. Rev. Biochem. . 68 . 287–300 . 1999 . 10872451 . 10.1146/annurev.biochem.68.1.287 .
9. Zhong. C. Zhang. S. Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment.. Nucleic Acids Research. Feb 2012. 40. 3. 1307–17. 21976732. 10.1093/nar/gkr804. 3273805.
10. Lee. JC. Gutell. RR. Russell. R. The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions.. Journal of Molecular Biology. Jul 28, 2006. 360. 5. 978–88. 16828489. 10.1016/j.jmb.2006.05.066.