2idn: Difference between revisions
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New page: left|200px<br /><applet load="2idn" size="350" color="white" frame="true" align="right" spinBox="true" caption="2idn" /> '''NMR structure of a new modified Thrombin Bin... |
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== | ==NMR structure of a new modified Thrombin Binding Aptamer containing a 5'-5' inversion of polarity site== | ||
The solution structure of a new modified thrombin binding aptamer (TBA) | <StructureSection load='2idn' size='340' side='right'caption='[[2idn]]' scene=''> | ||
== Structural highlights == | |||
<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> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> | |||
<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> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 2idn" style="background-color:#fffaf0;"></div> | ||
[[Category: Giancola | == References == | ||
[[Category: Martino | <references/> | ||
[[Category: Mayol | __TOC__ | ||
[[Category: Randazzo | </StructureSection> | ||
[[Category: Virno | [[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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