ISDA: 2IDN

Deposition Date 2006-09-15

Release Date 2007-01-09

Last Version Date 2024-05-29

Entry Detail

PDB ID:

2IDN

Keywords:

DNA

Title:

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

Biological Source:

Source Organism:

Method Details:

Experimental Method:

SOLUTION NMR

Conformers Calculated:

Conformers Submitted:

Selection Criteria:

structures with the lowest energy

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:3'-D(P*GP*G*T)-5'-5'-D(P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'
Chain IDs:A
Chain Length:15
Number of Molecules:1
Biological Source:

Ligand Molecules

Primary Citation

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

Martino, L, Virno, A, Randazzo, A, Virgilio, A, Esposito, V, Giancola, C, Bucci, M, Cirino, G, Mayol, L.Show

Nucleic Acids Res. 34 6653 6662 (2006)

PMID: 17145716 DOI: 10.1093/nar/gkl915

Abstact

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.

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Primary Citation of related structures

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