SOLUTION STRUCTURE OF AN ATP-BINDING RNA APTAMER REVEALS A NOVEL FOLD

In vitro selection has been used to isolate several RNA aptamers that bind specifically to biological cofactors. A well-characterized exampl e is the ATP-binding RNA aptamer family, which contains a conserved 11 -base loop opposite a bulged G and flanked by regions of double-strand ed RNA. The nucleotides in the consensus sequence provide a binding po cket for ATP (or AMP), which binds with a K-d in the micromolar range. Here we present the three-dimensional solution structure of a 36-nucl eotide ATP-binding RNA aptamer complexed with AMP, determined from NMR -derived distance and dihedral angle restraints. The conserved loop an d bulged G form a novel compact, folded structure around the AMP. The backbone tracing of the loop nucleotides can be described by a Greek z eta (zeta). Consecutive loop nucleotides G, A, A form a U-turn at the bottom of the zeta, and interact with the AMP to form a structure simi lar to a GNRA tetraloop, with AMP standing in for the final A. Two asy mmetric G . G base pairs close the stems flanking the internal loop. M utated aptamers support the existence of the tertiary interactions wit hin the consensus nucleotides and with the AMP found in the calculated structures.