internal loop

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,{{cite journal|last1=Lescoute|first1=A|last2=Leontis|first2=NB|last3=Massire|first3=C|last4=Westhof|first4=E|title=Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments.|journal=Nucleic Acids Research|date=2005|volume=33|issue=8|pages=2395–409|pmid=15860776|doi=10.1093/nar/gki535|pmc=1087784}}

the docking-elbow,{{cite journal|last1=Lehmann|first1=J|last2=Jossinet|first2=F|last3=Gautheret|first3=D|title=A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders.|journal=Nucleic Acids Research|date=May 1, 2013|volume=41|issue=10|pages=5494–502|pmid=23580544|doi=10.1093/nar/gkt219|pmc=3664808}}

kink-turns (k-turn),{{cite journal|last1=Klein|first1=D.J.|title=The kink-turn: a new RNA secondary structure motif|journal=The EMBO Journal|volume=20|issue=15|year=2001|pages=4214–4221|issn=1460-2075|doi=10.1093/emboj/20.15.4214|pmc=149158|pmid=11483524}}{{cite journal|last1=Schroeder|first1=KT|last2=McPhee|first2=SA|last3=Ouellet|first3=J|last4=Lilley|first4=DM|title=A structural database for k-turn motifs in RNA.|journal=RNA|date=Aug 2010|volume=16|issue=8|pages=1463–8|pmid=20562215|doi=10.1261/rna.2207910|pmc=2905746}}

the right-angle,{{cite journal|last1=Grabow|first1=WW|last2=Zhuang|first2=Z|last3=Swank|first3=ZN|last4=Shea|first4=JE|last5=Jaeger|first5=L|title=The right angle (RA) motif: a prevalent ribosomal RNA structural pattern found in group I introns.|journal=Journal of Molecular Biology|date=Nov 23, 2012|volume=424|issue=1–2|pages=54–67|pmid=22999957|doi=10.1016/j.jmb.2012.09.012|pmc=3488136}}

the sarcin/ricin loops (also called bulged-G motifs),{{cite journal|last1=Szewczak|first1=AA|last2=Moore|first2=PB|title=The sarcin/ricin loop, a modular RNA.|journal=Journal of Molecular Biology|date=Mar 17, 1995|volume=247|issue=1|pages=81–98|pmid=7897662|doi=10.1006/jmbi.1994.0124|doi-access=free}}{{cite journal|last1=Leontis|first1=NB|last2=Westhof|first2=E|title=A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs.|journal=Journal of Molecular Biology|date=Oct 30, 1998|volume=283|issue=3|pages=571–83|pmid=9784367|doi=10.1006/jmbi.1998.2106}}{{cite journal |author=Moore PB |title=Structural motifs in RNA |journal=Annu. Rev. Biochem. |volume=68 |pages=287–300 |year=1999 |pmid=10872451 |doi=10.1146/annurev.biochem.68.1.287 }}

the twist-up motif{{cite journal|last1=Zhong|first1=C|last2=Zhang|first2=S|title=Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment.|journal=Nucleic Acids Research|date=Feb 2012|volume=40|issue=3|pages=1307–17|pmid=21976732|doi=10.1093/nar/gkr804|pmc=3273805}}

and the UAA/GAN internal loop motif.{{cite journal|last1=Lee|first1=JC|last2=Gutell|first2=RR|last3=Russell|first3=R|title=The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions.|journal=Journal of Molecular Biology|date=Jul 28, 2006|volume=360|issue=5|pages=978–88|pmid=16828489|doi=10.1016/j.jmb.2006.05.066}}

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| title = Gallery of RNA motifs that host internal loops

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| File:C-loop-secondary-structure.svg|A consensus secondary structure and primary sequence for the C-loop RNA motif.

| File:Docking elbow-secondary-structure.svg|A consensus secondary structure and primary sequence for the docking elbow RNA motif.

| File:K-turn-1-secondary-structure.svg|A consensus secondary structure and primary sequence for the kink-turn RNA motif.

| File:K-turn-2-secondary-structure.svg|A consensus secondary structure and primary sequence for the kink-turn RNA motif.

| File:Right angle-2-secondary-structure.svg|A consensus secondary structure and primary sequence for the right-angle RNA motif.

| File:Sarcin-ricin-1-secondary-structure.svg|A consensus secondary structure and primary sequence for the 3` Sarcin-Ricin (or bulged-G) RNA motif.

| File:Sarcin-ricin-2-secondary-structure.svg|A consensus secondary structure and primary sequence for the 5` Sarcin-Ricin (or bulged-G) RNA motif.

| File:Twist up-secondary-structure.svg|A consensus secondary structure and primary sequence for the twist-up RNA motif.

| File:UAA GAN-secondary-structure.svg|A consensus secondary structure and primary sequence for the UAA-GAN RNA motif.

|}}

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