2arg

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FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES

Overview

BACKGROUND: In vitro selection has identified DNA aptamers that target, cofactors, amino acids, peptides and proteins. Structure determination 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 approximately 100 microM affinity. RESULTS: The DNA, aptamer generates its L-argininamide-binding pocket by adaptive zippering, up the 18-residue loop through formation of Watson-Crick pairs, mismatch, pairs and base triples, while maximizing stacking interactions. Three of, the four base triples involve minor-groove recognition through sheared G.A, mismatch formation. The unique fold is also achieved through positioning, of an adenine residue deep within the minor groove and through nestling of, a smaller loop within the larger loop on complex formation. The, accessibility to the unique L-argininamide-binding pocket is restricted by, a base pair that bridges across one side of the major-groove-binding site., The guanidinium group of the bound L-argininamide aligns through, intermolecular hydrogen-bond formation with the base edges of nonadjacent, guanine and cytosine residues while being sandwiched between the planes of, nonadjacent guanine residues. CONCLUSIONS: The available structures of, L-arginine/L-argininamide bound to their DNA and RNA targets define the, common principles and patterns associated with molecular recognition, as, well as the diversity of intermolecular hydrogen-bonding alignments, associated with the distinct binding pockets.

About this Structure

2ARG is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.

Reference

Formation of an amino-acid-binding pocket through adaptive zippering-up of a large DNA hairpin loop., Lin CH, Wang W, Jones RA, Patel DJ, Chem Biol. 1998 Oct;5(10):555-72. PMID:9818148

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