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J. Biol. Chem., Vol. 277, Issue 3, 2104-2111, January 18, 2002

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Adenine-Aptamer Complexes
A BIPARTITE RNA SITE THAT BINDS THE ADENINE NUCLEIC BASE^*

Marc Meli, Jacques Vergne, Jean-Luc Décout^§, and Marie-Christine Maurel^¶

From the  Institut Jacques Monod, Laboratoire de Biochimie de l'Evolution et Adaptabilité Moléculaire, Tour 43, 2 place Jussieu, 75251 Paris Cedex 05, France and the ^§ Laboratoire de Chimie Bio-organique Département de Pharmacochimie Moléculaire, UMR 5063 CNRS/Université Joseph Fourier-Grenoble I, Domaine de la Merci, 38706 La Tronche Cedex, France

RNA aptamers that are able to complex free adenine have been isolated by a SELEX (systematic evolution of ligands by exponential enrichment) procedure. The adenine binding site was revealed by sequence alignment for a prevalent cluster of aptamers, and its structure and interactions with adenine were probed by RNase digestion studies, lead cleavage, boundary determination experiments, and truncated sequences studies. A new purine binding motif was functionally and structurally characterized and compared with other RNAs specific to purine or adenylated compounds. The affinity for adenine and the specificity for other related targets were quantified. This work suggests that the adenine binding site is composed of two independent secondary structure elements forming a bipartite binding site that interacts with adenine in a new mode of purine recognition. Such binding is of great interest because the imidazole moiety is not trapped in the binding site, and would easily be available for catalytic activity.

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