Three Small Ribooligonucleotides with Specific Arginine Sites

Arginine-binding RNA motifs are important to protein-RNA interaction and perhaps also for Archean biochemistry. Selection-amplification was used to isolate three RNAs that are eluted by free arginine from an l-arginine affinity column (K_d ≈ 0.2–0.4 mM). The binding sites contain specific internal and bulge loops, whose sequences can include arginine coding triplets. Binding is highly specific for arginine, but all three motifs, like the self-splicing group I intron, also bind guanosine 5′-monophosphate. One site is stereoselective, somewhat preferring d-arginine.