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Science 31 May 1996:
Vol. 272. no. 5266, pp. 1343 - 1347
DOI: 10.1126/science.272.5266.1343
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Reports

Structural Basis of Ligand Discrimination by Two Related RNA Aptamers Resolved by NMR Spectroscopy

Yinshan Yang, Michel Kochoyan, * Petra Burgstaller, Eric Westhof, Michael Famulok

In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket.

Y. Yang, Centre de Biochimie Structurale (CBS), Unité Mixte de Recherche CNRS 9955, INSERM U414, Faculté de Pharmacie, 15 Avenue Ch. Flahault, 34060 Montpellier, France.
M. Kochoyan, CBS Faculté de Pharmacie, 15 Avenue Ch. Flahault, 34060 Montpellier, and Groupe de Biophysique, Unité de Recherche Associée CNRS D1254, Ecole Polytechnique, Route de Saclay, 91128 Palaiseau, France.
P. Burgstaller and M. Famulok, Institut für Biochemie der Ludwig Maximillians Universität München-Genzentrum, Würmtalstradße 221, 81375 München, Germany.
E. Westhof, Institut de Biologie Moléculaire et Cellulaire, Unité Propre de Recherche CNRS 9002, 15 Rue R. Descartes, 67084 Strasbourg Cedex, France.
* To whom correspondence should be addressed. E-mail: michel{at}tome.cbs.univ-montp1.fr


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