1p3x

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==INTRAMOLECULAR DNA TRIPLEX WITH 1-PROPYNYL DEOXYURIDINE IN THE THIRD STRAND, NMR, 10 STRUCTURES==
==INTRAMOLECULAR DNA TRIPLEX WITH 1-PROPYNYL DEOXYURIDINE IN THE THIRD STRAND, NMR, 10 STRUCTURES==
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<StructureSection load='1p3x' size='340' side='right' caption='[[1p3x]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
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<StructureSection load='1p3x' size='340' side='right'caption='[[1p3x]]' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[1p3x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P3X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P3X FirstGlance]. <br>
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<table><tr><td colspan='2'>[[1p3x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P3X FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PDU:5(1-PROPYNYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>PDU</scene><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><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene></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=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene>, <scene name='pdbligand=PDU:5(1-PROPYNYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>PDU</scene></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p3x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p3x RCSB], [http://www.ebi.ac.uk/pdbsum/1p3x PDBsum]</span></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=1p3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p3x OCA], [https://pdbe.org/1p3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p3x RCSB], [https://www.ebi.ac.uk/pdbsum/1p3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p3x ProSAT]</span></td></tr>
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<table>
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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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Incorporation of the modified base 5-(1-propynl)-2'-deoxyuridine (propynylU) in the third strand of a triplex leads to enhanced triplex stabilization. To investigate effects of the propyne nucleotide on triplex structure and the factors underlying the increased stability, we have determined the solution structure of the intramolecular DNA pyrmidine-purine-pyrimdine d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-PCPCPCPP) (PDD-EG), which contains 5-(1-propynl)-2'-deoxyuridine (P) in the third strand and hexakis(ethylene glycol) linkers [(EG)6]. The structure was calculated using X-PLOR with distance and dihedral angle restraints obtained from two-dimensional NMR experiments and refined with the direct relaxation matrix method. The structures show that the extended aromatic electron cloud of the propynylU nucleotide stacks well over the 5'-neighboring nucleotides, resulting in increased stabilization. The propynylU nucleotides also affect the overall structure of the triple helix. A comparison of the structure to that of the nonmodified intramolecular DNA triplex of the same sequence, d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT) (DDD-EG), shows that PDD-EG has a more A-DNA like X displacement and inclination than DDD-EG yet still maintains predominantly S-type sugar puckers as found in DDD-EG and other DNA triplexes.
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Solution structure of an intramolecular DNA triplex containing 5-(1-propynyl)-2'-deoxyuridine residues in the third strand.,Phipps AK, Tarkoy M, Schultze P, Feigon J Biochemistry. 1998 Apr 28;37(17):5820-30. PMID:9558315<ref>PMID:9558315</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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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Feigon, J.]]
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[[Category: Large Structures]]
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[[Category: Phipps, A K.]]
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[[Category: Feigon J]]
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[[Category: Schultze, P.]]
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[[Category: Phipps AK]]
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[[Category: Tarkoy, M.]]
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[[Category: Schultze P]]
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[[Category: Dna]]
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[[Category: Tarkoy M]]
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[[Category: Oligonucleotide]]
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[[Category: Propyne]]
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[[Category: Triplex]]
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INTRAMOLECULAR DNA TRIPLEX WITH 1-PROPYNYL DEOXYURIDINE IN THE THIRD STRAND, NMR, 10 STRUCTURES

PDB ID 1p3x

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