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1d3r

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==CRYSTAL STRUCTURE OF TRIPLEX DNA==
==CRYSTAL STRUCTURE OF TRIPLEX DNA==
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<StructureSection load='1d3r' size='340' side='right' caption='[[1d3r]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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<StructureSection load='1d3r' size='340' side='right'caption='[[1d3r]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[1d3r]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D3R FirstGlance]. <br>
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<table><tr><td colspan='2'>[[1d3r]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D3R FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>
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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]] 1.8&#8491;</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=1d3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d3r RCSB], [http://www.ebi.ac.uk/pdbsum/1d3r PDBsum]</span></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=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>
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<table>
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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=1d3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3r OCA], [https://pdbe.org/1d3r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d3r RCSB], [https://www.ebi.ac.uk/pdbsum/1d3r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d3r ProSAT]</span></td></tr>
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<div style="background-color:#fffaf0;">
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</table>
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== Publication Abstract from PubMed ==
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Extended purine sequences on a DNA strand can lead to the formation of triplex DNA in which the third strand runs parallel to the purine strand. Triplex DNA structures have been proposed to play a role in gene expression and recombination and also have potential application as antisense inhibitors of gene expression. Triplex structures have been studied in solution by NMR, but have hitherto resisted attempts at crystallization. Here, we report a novel design of DNA sequences, which allows the first crystallographic study of DNA segment containing triplexes and its junction with a duplex. In the 1.8 A resolution structure, the sugar-phosphate backbone of the third strand is parallel to the purine-rich strand. The bases of the third strand associate with the Watson and Crick duplex via Hoogsteen-type interactions, resulting in three consecutive C(+).GC, BU.ABU (BU = 5-bromouracil), and C(+).GC triplets. The overall conformation of the DNA triplex has some similarity to the B-form, but is distinct from both A- and B-forms. There are large changes in the phosphate backbone torsion angles (particularly gamma) of the purine strand, probably due to the electrostatic interactions between the phosphate groups and the protonated cytosine. These changes narrow the minor groove width of the purine-Hoogsteen strands and may represent sequence-specific structural variations of the DNA triplex.
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Structure of a triple helical DNA with a triplex-duplex junction.,Rhee S, Han Z, Liu K, Miles HT, Davies DR Biochemistry. 1999 Dec 21;38(51):16810-5. PMID:10606513<ref>PMID:10606513</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: Davies, D R.]]
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[[Category: Large Structures]]
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[[Category: Han, Z J.]]
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[[Category: Davies DR]]
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[[Category: Liu, K.]]
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[[Category: Han Z-J]]
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[[Category: Miles, H T.Todd.]]
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[[Category: Liu K]]
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[[Category: Rhee, S.]]
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[[Category: Rhee S]]
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[[Category: Dna]]
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[[Category: Todd Miles HT]]
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[[Category: Triplex dna and its junction with a duplex dna]]
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Current revision

CRYSTAL STRUCTURE OF TRIPLEX DNA

PDB ID 1d3r

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