2IDN

NMR structure of a new modified Thrombin Binding Aptamer containing a 5'-5' inversion of polarity site

Summary for 2IDN

• Entry DOI: 10.2210/pdb2idn/pdb
• Descriptor: 3'-D(P*GP*G*T)-5'-5'-D(P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3' (1 entity in total)
• Functional Keywords: inversion of polarity, tba, anticoagulant, dna, quadruplex, 5'-5'
• Total number of polymer chains: 1
• Total formula weight: 4743.05

Authors

Randazzo, A.,Martino, L.,Virno, A.,Mayol, L.,Giancola, C. (deposition date: 2006-09-15, release date: 2007-01-09, Last modification date: 2024-05-29)

Primary citation

Martino, L.,Virno, A.,Randazzo, A.,Virgilio, A.,Esposito, V.,Giancola, C.,Bucci, M.,Cirino, G.,Mayol, L.
A new modified thrombin binding aptamer containing a 5'-5' inversion of polarity site.
Nucleic Acids Res., 34:6653-6662, 2006

PubMed 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.

PubMed: 17145716
DOI: 10.1093/nar/gkl915

Experimental method

SOLUTION NMR