2idn

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|PDB= 2idn |SIZE=350|CAPTION= <scene name='initialview01'>2idn</scene>
|PDB= 2idn |SIZE=350|CAPTION= <scene name='initialview01'>2idn</scene>
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|SITE=
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|LIGAND= <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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|ACTIVITY=
|GENE=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2idn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2idn OCA], [http://www.ebi.ac.uk/pdbsum/2idn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2idn RCSB]</span>
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[[Category: tba]]
[[Category: tba]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:28:14 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:42:52 2008''

Revision as of 00:42, 31 March 2008

Image:2idn.gif


PDB ID 2idn

Drag the structure with the mouse to rotate
Ligands: ,
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



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


Overview

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.

About this Structure

2IDN is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

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, Nucleic Acids Res. 2006;34(22):6653-62. Epub 2006 Dec 1. PMID:17145716

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