Examples of modular RNA sequences isolated from SELEX. Capital letters indicate initially random regions, while lower-case letters indicate fixed regions such as primer complements. Critical motifs are highlighted in bold. Diagrams at right show the motifs in their required structural context for the active site. Numbers in brackets indicate the position where the displayed sequence begins; ellipsis indicates that the sequence continues 3′ from the displayed region. (A) The minimal isoleucine motif (Majerfeld and Yarus 1998); although the conserved CUAC was originally found in the 5′ primer, subsequent reselection recovered this module from random sequence (S. Changayil and M. Yarus, pers. comm.), giving a total of 12 bases in two modules. If paired but otherwise unspecified regions are included, the site increases to 18 bases in two modules. (B) The hammerhead ribozyme, reselected from random sequence (Salehi-Ashtiani and Szostak 2001). The single U that comprises module 1 was supplied in a constant region; x marks the cleavage site. Thus, the hammerhead consists of 11 fixed nucleotides in three modules (the GC pair shown in plan text is conserved in natural hammerhead sequences, but was not recovered in SELEX). If paired but otherwise unspecified regions are included, this increases to 37 fixed nucleotides in three modules. Note that this upper limit is unrealistically large, because there are many possible sequences compatible with the required paired regions.
