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[[Image:2idn.gif|left|200px]]


{{Structure
==NMR structure of a new modified Thrombin Binding Aptamer containing a 5'-5' inversion of polarity site==
|PDB= 2idn |SIZE=350|CAPTION= <scene name='initialview01'>2idn</scene>
<StructureSection load='2idn' size='340' side='right'caption='[[2idn]]' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
<table><tr><td colspan='2'>[[2idn]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IDN FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
|GENE=  
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2idn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2idn OCA], [https://pdbe.org/2idn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2idn RCSB], [https://www.ebi.ac.uk/pdbsum/2idn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2idn ProSAT]</span></td></tr>
|DOMAIN=
</table>
|RELATEDENTRY=
<div style="background-color:#fffaf0;">
|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>
== Publication Abstract from PubMed ==
}}
 
'''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.
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==
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<ref>PMID:17145716</ref>
2IDN is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IDN 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:[http://www.ncbi.nlm.nih.gov/pubmed/17145716 17145716]
[[Category: Protein complex]]
[[Category: Giancola, C.]]
[[Category: Martino, L.]]
[[Category: Mayol, L.]]
[[Category: Randazzo, A.]]
[[Category: Virno, A.]]
[[Category: 5'-5s']]
[[Category: anticoagulant]]
[[Category: dna]]
[[Category: inversion of polarity]]
[[Category: quadruplex]]
[[Category: tba]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:42:52 2008''
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2idn" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Giancola C]]
[[Category: Martino L]]
[[Category: Mayol L]]
[[Category: Randazzo A]]
[[Category: Virno A]]

Latest revision as of 16:38, 13 December 2023

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

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