RNA libraries and RNA recognition

Random RNA libraries, consisting of > 10(13) unique sequences, contain molecules capable of specifically binding small molecule and protein ligands by noncovalent interaction. Successive steps of affinity purification and amplification allow the propagation and eventual isolation of specific binding molecules, called aptamers. Although protein- and small-molecule-binding aptamers have been characterized previously, selection of RNA aptamers capable of binding nucleic acids has previously yielded only molecules capable of Watson-Crick base pairing to the nucleic acid ligand used for selection. On the other hand, it is known from studies on catalytic and other RNAs that both inter- and intramolecular RNA-RNA interaction can occur by non-Watson-Crick means. We have therefore incorporated a strategy to obviate the possibility of Watson-Crick interaction into a selection scheme for the isolation of RNA-recognizing aptamers. The aptamers so isolated do not show extensive Watson-Crick complementarity with the RNA ligand used for the selection, thereby validating the selection strategy. Curiously, all of the aptamers characterized contain several oligo-G stretches bounded by U residues. This sequence motif, which occurs as DNA in telomeres (chromosome ends) may therefore be a general RNA-RNA interaction motif. An additional sequence motif is apparently superimposed on this background structure.