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2idn

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(New page: 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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[[Image:2idn.gif|left|200px]]<br /><applet load="2idn" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2idn" />
 
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'''NMR structure of a new modified Thrombin Binding Aptamer containing a 5'-5' inversion of polarity site'''<br />
 
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==Overview==
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==NMR structure of a new modified Thrombin Binding Aptamer containing a 5'-5' inversion of polarity site==
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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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<StructureSection load='2idn' size='340' side='right'caption='[[2idn]]' scene=''>
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== Structural highlights ==
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<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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<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>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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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==About this Structure==
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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>
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2IDN is a [http://en.wikipedia.org/wiki/Protein_complex 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].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17145716 17145716]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 2idn" style="background-color:#fffaf0;"></div>
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[[Category: Giancola, C.]]
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== References ==
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[[Category: Martino, L.]]
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<references/>
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[[Category: Mayol, L.]]
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__TOC__
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[[Category: Randazzo, A.]]
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</StructureSection>
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[[Category: Virno, A.]]
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[[Category: Large Structures]]
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[[Category: 5'-5']]
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[[Category: Giancola C]]
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[[Category: anticoagulant]]
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[[Category: Martino L]]
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[[Category: dna]]
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[[Category: Mayol L]]
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[[Category: inversion of polarity]]
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[[Category: Randazzo A]]
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[[Category: quadruplex]]
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[[Category: Virno A]]
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[[Category: tba]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:39:22 2008''
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Current revision

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

PDB ID 2idn

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