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Nucleic Acids Research 2004 32(17):5045-5058; doi:10.1093/nar/gkh835
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Published online 27 September 2004

Nucleic Acids Research, Vol. 32 No. 17 © Oxford University Press 2004; all rights reserved

Selection and evolution of NTP-specific aptamers

Laure Weill, Dominique Louis and Bruno Sargueil*

Centre de Génétique Moléculaire, CNRS, Avenue de la Terrasse, 91190 Gif sur Yvette, France

* To whom correspondence should be addressed. Tel: +33 1 69 82 31 54; Fax: +33 1 69 82 43 86; Email: sargueil{at}cgm.cnrs-gif.fr
Present address: Dominique Louis, EVOLOGIC, 2, rue Gaston Crémieux, 91000 EVRY, France
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Received March 29, 2004; Revised April 29, 2004; Accepted September 1, 2004

ATP occupies a central position in biology, for it is both an elementary building block of RNA and the most widely used cofactor in all living organisms. For this reason, it has been a recurrent target for in vitro molecular evolution techniques. The exploration of ATP-binding motifs constitutes both an important step in investigating the plausibility of the ‘RNA world’ hypothesis and a central starting point for the development of new enzymes. To date, only two RNA motifs that bind ATP have been characterized. The first one is targeted to the adenosine moiety, while the second one recognizes the ‘Hoogsteen’ face of the base. To isolate aptamers that bind ATP in different orientations, we selected RNAs on an affinity resin that presents ATP in three different orientations. We obtained five new motifs that were characterized and subsequently submitted to a secondary selection protocol designed to isolate aptamers specific for cordycepin. Interestingly, all the ATP-binding motifs selected specifically recognize the sugar-phosphate backbone region of the nucleotides. Three of the aptamers show some selectivity for adenine derivatives, while the remainder recognize any of the four nucleotides with similar efficiency. The characteristics of these aptamers are discussed along with implications for in vitro molecular evolution.


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