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Nucleic Acids Res. 2006;34(22):6653-62. Epub 2006 Dec 1.

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

Author information

1
Dipartimento di Chimica, Università degli Studi di Napoli Federico II, via Cintia, I-80126, Napoli, Italy.

Abstract

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 degrees 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.

PMID:
17145716
PMCID:
PMC1751544
DOI:
10.1093/nar/gkl915
[Indexed for MEDLINE]
Free PMC Article

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