Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 12 (December 2013)


research papers



Acta Cryst. (2013). D69, 2403-2411    [ doi:10.1107/S0907444913022269 ]

Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer

I. Russo Krauss, A. Pica, A. Merlino, L. Mazzarella and F. Sica

Abstract: Potent second-generation thrombin aptamers adopt a duplex-quadruplex bimodular folding and recognize thrombin exosite II with very high affinity and specificity. A sound model of these oligonucleotides, either free or in complex with thrombin, is not yet available. Here, a structural study of one of these aptamers, HD22-27mer, is presented. The crystal structure of this aptamer in complex with thrombin displays a novel architecture in which the helical stem is enchained to a pseudo-G-quadruplex. The results also underline the role of the residues that join the duplex and quadruplex motifs and control their recruitment in thrombin binding.

PDB reference: 4i7y

Keywords: thrombin; aptamers; duplex-quadruplex motifs.


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[ doi:10.1107/S0907444913022269/mh5101sup1.pdf ]
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