SELECTION OF AN RNA DOMAIN THAT BINDS ZN2+

We have selected an RNA that depends on zinc for affinity to a column, starting from a pool of ribooligonucleotides with 50 randomized posit ions. This RNA's chemical sensitivities, calculated folding thermodyna mics, and activity when fragmented suggest that an ion binding site li es within a complex 21-nt hairpin loop, near the junction with an impe rfect helical stem. This RNA site has an unselected selectivity among divalents, preferring nickel, cobalt, and cadmium to calcium, magnesiu m, and manganese, as expected for a simple site of chelation. A modera te zinc-dependent change in loop structure accompanies divalent bindin g and can be detected by chemical probing and zinc-dependent UV-induce d crosslinking. The latter also demonstrates the apposition of loop se quences to make a structure that may be related to the E-loop motif fo und in a number of other RNA molecules; the E-loop motif, accordingly, may be a divalent site.