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

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.

SUBMITTER: Martino L 

PROVIDER: S-EPMC1751544 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature

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

Martino Luigi L   Virno Ada A   Randazzo Antonio A   Virgilio Antonella A   Esposito Veronica V   Giancola Concetta C   Bucci Mariarosaria M   Cirino Giuseppe G   Mayol Luciano L  

Nucleic acids research 20061201 22

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  ...[more]

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