Editing Inverted repeat (section)

===Inverted repeats in pseudoknots===
[[Pseudoknot]]s are common structural motifs found in RNA.  They are formed by two nested [[stem-loop]]s such that the stem of one structure is formed from the loop of the other.  There are multiple folding [[topology|topologies]] among pseudoknots and great variation in loop lengths, making them a structurally diverse group.<ref name=Staple>{{cite journal|last=Staple|first=DW|author2=Butcher, SE|title=Pseudoknots: RNA structures with diverse functions.|journal=PLOS Biology|date=June 2005|volume=3|issue=6|pages=e213|pmid=15941360|doi=10.1371/journal.pbio.0030213|pmc=1149493 |doi-access=free }} {{open access}}</ref>

Inverted repeats are a key component of pseudoknots as can be seen in the illustration of a naturally occurring pseudoknot found in the human [[telomerase RNA component]].<ref name=chen-greider>{{cite journal|last=Chen|first=JL|author2=Greider, CW|title=Functional analysis of the pseudoknot structure in human telomerase RNA.|journal=Proceedings of the National Academy of Sciences of the United States of America|date=Jun 7, 2005|volume=102|issue=23|pages=8080–5; discussion 8077–9|pmid=15849264|doi=10.1073/pnas.0502259102|pmc=1149427|bibcode=2005PNAS..102.8080C|doi-access=free}}</ref> Four different sets of inverted repeats are involved in this structure.  Sets 1 and 2 are the stem of stem-loop A and are part of the loop for stem-loop B.  Similarly, sets 3 and 4 are the stem for stem-loop B and are part of the loop for stem-loop A.

Pseudoknots play a number of different roles in biology.  The telomerase pseudoknot in the illustration is critical to that enzyme's activity.<ref name=chen-greider />  The [[ribozyme]] for the [[Hepatitis D|''hepatitis delta virus (HDV)'']] folds into a double-pseudoknot structure and self-cleaves its circular genome to produce a single-genome-length RNA.  Pseudoknots also play a role in programmed [[ribosomal frameshift]]ing found in some viruses and required in the replication of [[retroviruses]].<ref name=Staple />{{Clear}}