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Acta Crystallogr D Biol Crystallogr. 2013 Dec;69(Pt 12):2403-11. doi: 10.1107/S0907444913022269. Epub 2013 Nov 19.

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

Author information

1
Department of Chemical Sciences, University of Naples `Federico II', Complesso Universitario di Monte Sant'Angelo, I-80126 Naples, Italy.

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.

KEYWORDS:

aptamers; duplex–quadruplex motifs; thrombin

PMID:
24311581
DOI:
10.1107/S0907444913022269
[Indexed for MEDLINE]

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