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Nucleic Acids Research Advance Access originally published online on December 1, 2006
Nucleic Acids Research 2006 34(22):6653-6662; doi:10.1093/nar/gkl915
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Nucleic Acids Research, 2006, Vol. 34, No. 22 6653-6662
© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

A new modified thrombin binding aptamer containing a 5'–5' inversion of polarity site

Luigi Martino, Ada Virno1, Antonio Randazzo1, Antonella Virgilio1, Veronica Esposito1, Concetta Giancola, Mariarosaria Bucci2, Giuseppe Cirino2 and Luciano Mayol1,*

Dipartimento di Chimica, Università degli Studi di Napoli ‘Federico II’ via Cintia, I-80126, Napoli, Italy 1 Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli ‘Federico II’ via D. Montesano 49, I-80131 Napoli, Italy 2 Dipartimento di Farmacologia Sperimentale, Università degli Studi di Napoli ‘Federico II’ via D. Montesano 49, I-80131 Napoli, Italy

*To whom correspondence should be addressed. Tel: +39 081 678508; Fax: +39 081 678552; Email: mayoll{at}unina.it

Received July 31, 2006. Revised October 16, 2006. Accepted October 17, 2006.

The solution structure of a new modified thrombin binding aptamer (TBA) containing a 5'–5' inversion of polarity site, namely d(3'GGT5'-5'TGGTGTGGTTGG3'), is reported. NMR and CD spectroscopy, as well as molecular dynamic and mechanic calculations, have been used to characterize the 3D structure. The modified oligonucleotide is characterized by a chair-like structure consisting of two G-tetrads connected by three edge-wise TT, TGT and TT loops. d(3'GGT5'-5'TGGTGTGGTTGG3') is characterized by an unusual folding, being three strands parallel to each other and only one strand oriented in opposite manner. This led to an anti-anti-anti-syn and syn-syn-syn-anti arrangement of the Gs in the two tetrads. The thermal stability of the modified oligonucleotide is 4°C higher than the corresponding unmodified TBA. d(3'GGT5'-5'TGGTGTGGTTGG3') continues to display an anticoagulant activity, even if decreased with respect to the TBA.

Dedicated to the memory of Prof. Luigi Gomez-Paloma


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