Hairpin Ribozyme: Difference between revisions

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The secondary structure of the hairpin ribozyme contains two independently folding domains, called A and B.  In each domain there is an internal loop flanked by two helices(H1 and H2 in domain A and H3 and H4 in domain B).  The RNA substrate is bound in domain A through Watson-Crick base pairs in H1 and H2.  Once bound to domain A, the substrate is reversibly cleaved.  Linkers of varying lengths were inserted between the 5' end of the substrate and the 3' end of the ribozyme in order to test what proximity is preferred by the two domains.  The results of the test showed that the two domains prefer to be relatively close to one another and use H2 and H3 as a sort of hinge.  In the naturally occurring hairpin ribozyme, this hinge is occupied by a four-way junction, which is believed to regulate inter-domain interactions by alternative stacking of helices.<ref>PMID: 9667918</ref>