3opi

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[[Image:3opi.png|left|200px]]
 
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==7-DEAZA-2'-DEOXYADENOSINE modification in B-FORM DNA==
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The line below this paragraph, containing "STRUCTURE_3opi", creates the "Structure Box" on the page.
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<StructureSection load='3opi' size='340' side='right'caption='[[3opi]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3opi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OPI 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">X-ray diffraction, [[Resolution|Resolution]] 1.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7DA:7-DEAZA-2-DEOXYADENOSINE-5-MONOPHOSPHATE'>7DA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_3opi| PDB=3opi | SCENE= }}
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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=3opi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3opi OCA], [https://pdbe.org/3opi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3opi RCSB], [https://www.ebi.ac.uk/pdbsum/3opi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3opi 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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As part of an ongoing effort to explore the effect of major groove electrostatics on the thermodynamic stability and structure of DNA, a 7-deaza-2'-deoxyadenosine:dT (7-deaza-dA:dT) base pair in the Dickerson-Drew dodecamer (DDD) was studied. The removal of the electronegative N7 atom on dA and the replacement with an electropositive C-H in the major groove was expected to have a significant effect on major groove electrostatics. The structure of the 7-deaza-dA:dT base pair was determined at 1.1 A resolution in the presence of Mg(2+). The 7-deaza-dA, which is isosteric for dA, had minimal effect on the base pairing geometry and the conformation of the DDD in the crystalline state. There was no major groove cation association with the 7-deaza-dA heterocycle. In solution, circular dichroism showed a positive Cotton effect centered at 280 nm and a negative Cotton effect centered at 250 nm that were characteristic of a right-handed helix in the B-conformation. However, temperature-dependent NMR studies showed increased exchange between the thymine N3 imino proton of the 7-deaza-dA:dT base pair and water, suggesting reduced stacking interactions and an increased rate of base pair opening. This correlated with the observed thermodynamic destabilization of the 7-deaza-dA modified duplex relative to the DDD. A combination of UV melting and differential scanning calorimetry experiments were conducted to evaluate the relative contributions of enthalpy and entropy in the thermodynamic destabilization of the DDD. The most significant contribution arose from an unfavorable enthalpy term, which probably results from less favorable stacking interactions in the modified duplex, which was accompanied by a significant reduction in the release of water and cations from the 7-deaza-dA modified DNA.
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===7-DEAZA-2'-DEOXYADENOSINE modification in B-FORM DNA===
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Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2'-deoxyadenosine:dT Base Pairing in DNA.,Kowal EA, Ganguly M, Pallan PS, Marky LA, Gold B, Egli M, Stone MP J Phys Chem B. 2011 Dec 1;115(47):13925-34. Epub 2011 Nov 8. PMID:22059929<ref>PMID:22059929</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_22059929}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3opi" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 22059929 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_22059929}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[3opi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OPI OCA].
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[[Category: Egli M]]
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[[Category: Ganguly M]]
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==Reference==
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[[Category: Gold B]]
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<ref group="xtra">PMID:022059929</ref><references group="xtra"/>
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[[Category: Kowal EA]]
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[[Category: Egli, M.]]
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[[Category: Marky LA]]
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[[Category: Ganguly, M.]]
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[[Category: Pallan PS]]
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[[Category: Gold, B.]]
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[[Category: Stone MP]]
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[[Category: Kowal, E A.]]
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[[Category: Marky, L A.]]
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[[Category: Pallan, P S.]]
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[[Category: Stone, M P.]]
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[[Category: 7-deaza-da]]
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[[Category: 7-deaza-deoxyadenosine]]
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[[Category: B-dna]]
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[[Category: Dna]]
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[[Category: Dodecamer]]
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Current revision

7-DEAZA-2'-DEOXYADENOSINE modification in B-FORM DNA

PDB ID 3opi

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