Small RNA-divalent domains.

From a potentially completely sampled set of randomized 23-mer sequences, we selected RNAs that bind a Zn-column and also show KD approximately 100-400 microM for free Zn2+, probably relying on one or two direct ion coordinations. Comparison of selected sequences with previously known divalent sites suggests three or four small RNA motifs repeatedly found to interact with divalent ions. We suggest that the GC cluster, the augmented GC cluster, and the E element may be useful generalized ion-binding structures. Such structures may help identify similar divalent sites in sequenced RNAs and serve as substructures for design of functional RNA metallodomains.