RNA aptamers that are able to complex free adenine have been isolated by a SELEX procedure. Adenine binding site was revealed by sequence alignment for a prevalent cluster of aptamers, its structure and its 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 to other RNA, specific to purine or adenylated compounds. The affinity for adenine and the specificity for other related targets were quantified. These works suggest 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 since the imidazole moiety is not trapped in the binding site and would easily be available for catalytic activity.