FORMATION OF AN AMINO-ACID-BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP

Background: in vitro selection has identified DNA aptamers that target cofactors, amino acids, peptides and proteins. Structure determinatio n of such ligand-DNA aptamer complexes should elucidate the details of adaptive DNA structural transitions, binding-pocket architectures and ligand recognition. We have determined the solution structure of the complex of a DNA aptamer containing a guanine-rich 18-residue hairpin loop that binds L-argininamide with similar to 100 mu M affinity. Resu lts: The DNA aptamer generates its L-argininamide-binding pocket by ad aptive zippering up the 18-residue loop through formation of Watson-Cr ick pairs, mismatch pairs and base triples, while maximizing stacking interactions. Three of the four base triples involve minor-groove reco gnition through sheared G.A mismatch formation. The unique fold is als o achieved through positioning of an adenine residue deep within the m inor groove and through nestling of a smaller loop within the larger l oop on complex formation. The accessibility to the unique L-argininami de-binding pocket is restricted by a base pair that bridges across one side of the major-groove-binding site. The guanidinium group of the b ound L-argininamide aligns through intermolecular hydrogen-bond format ion with the base edges of nonadjacent guanine and cytosine residues w hile being sandwiched between the planes of nonadjacent guanine residu es. Conclusions: The available structures of L-arginine/L-argininamide bound to their DNA and RNA targets define the common principles and p atterns associated with molecular recognition, as well as the diversit y of intermolecular hydrogen-bonding alignments associated with the di stinct binding pockets.