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 positions. This RNA's chemical sensitivities, calculated folding thermodynamics, and activity when fragmented suggest that an ion binding site lies within a complex 21-nt hairpin loop, near the junction with an imperfect helical stem. This RNA site has an unselected selectivity among divalents, preferring nickel, cobalt, and cadmium to calcium, magnesium, and manganese, as expected for a simple site of chelation. A moderate zinc-dependent change in loop structure accompanies divalent binding and can be detected by chemical probing and zinc-dependent UV-induced crosslinking. The latter also demonstrates the apposition of loop sequences to make a structure that may be related to the E-loop motif found in a number of other RNA molecules; the E-loop motif, accordingly, may be a divalent site.