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==Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir==
==Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir==
<StructureSection load='2l8p' size='340' side='right' caption='[[2l8p]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
<StructureSection load='2l8p' size='340' side='right'caption='[[2l8p]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2l8p]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L8P FirstGlance]. <br>
<table><tr><td colspan='2'>[[2l8p]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L8P FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=L8P:({[(2S)-1-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-3-HYDROXYPROPAN-2-YL]OXY}METHYL)PHOSPHONIC+ACID'>L8P</scene></td></tr>
</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2l8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l8p RCSB], [http://www.ebi.ac.uk/pdbsum/2l8p PDBsum]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=L8P:({[(2S)-1-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-3-HYDROXYPROPAN-2-YL]OXY}METHYL)PHOSPHONIC+ACID'>L8P</scene></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=2l8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8p OCA], [https://pdbe.org/2l8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l8p RCSB], [https://www.ebi.ac.uk/pdbsum/2l8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l8p ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cidofovir (1(S)-[3-hydroxy-2-(phosphonome-thoxy)propyl]cytosine, CDV) is a potent inhibitor of orthopoxvirus DNA replication. Prior studies have shown that, when CDV is incorporated into a growing primer strand, it can inhibit both the 3'-to-5' exonuclease and the 5'-to-3' chain extension activities of vaccinia virus DNA polymerase. This drug can also be incorporated into DNA, creating a significant impediment to trans-lesion DNA synthesis in a manner resembling DNA damage. CDV and deoxycytidine share a common nucleobase, but CDV lacks the deoxyribose sugar. The acyclic phosphonate bears a hydroxyl moiety that is equivalent to the 3'-hydroxyl of dCMP and permits CDV incorporation into duplex DNA. To study the structural consequences of inserting CDV into DNA, we have used (1)H NMR to solve the solution structures of a dodecamer DNA duplex containing a CDV molecule at position 7 and of a control DNA duplex. The overall structures of both DNA duplexes were found to be very similar. We observed a decrease of intensity (&gt;50%) for the imino protons neighboring the CDV (G6, T8) and the cognate base G18 and a large chemical shift change for G18. This indicates higher proton exchange rates for this region, which were confirmed using NMR-monitored melting experiments. DNA duplex melting experiments monitored by circular dichroism revealed a lower T(m) for the CDV DNA duplex (46 degrees C) compared to the control (58 degrees C) in 0.2 M salt. Our results suggest that the CDV drug is well accommodated and stable within the dodecamer DNA duplex, but the stability of the complex is less than that of the control, suggesting increased dynamics around the CDV.
Solution structure of a DNA duplex containing the potent anti-poxvirus agent cidofovir.,Julien O, Beadle JR, Magee WC, Chatterjee S, Hostetler KY, Evans DH, Sykes BD J Am Chem Soc. 2011 Feb 23;133(7):2264-74. Epub 2011 Jan 31. PMID:21280608<ref>PMID:21280608</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Beadle, J R.]]
[[Category: Large Structures]]
[[Category: Chatterjee, S.]]
[[Category: Beadle JR]]
[[Category: Evans, D H.]]
[[Category: Chatterjee S]]
[[Category: Hostetler, K Y.]]
[[Category: Evans DH]]
[[Category: Julien, O.]]
[[Category: Hostetler KY]]
[[Category: Magee, W C.]]
[[Category: Julien O]]
[[Category: Sykes, B D.]]
[[Category: Magee WC]]
[[Category: Dna]]
[[Category: Sykes BD]]
[[Category: Hpmpc]]
[[Category: Poxvirus]]

Latest revision as of 06:54, 1 May 2024

Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir

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