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New page: left|200px<br /><applet load="1v3n" size="450" color="white" frame="true" align="right" spinBox="true" caption="1v3n, resolution 1.8Å" /> '''Crystal structure of ...
 
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[[Image:1v3n.gif|left|200px]]<br /><applet load="1v3n" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1v3n, resolution 1.8&Aring;" />
'''Crystal structure of d(GCGAGAGC): the DNA quadruplex structure split from the octaplex'''<br />


==Overview==
==Crystal structure of d(GCGAGAGC): the DNA quadruplex structure split from the octaplex==
Recent genomic analyses revealed many kinds of tandem repeats of specific, sequences. Some of them are related to genetic diseases, but their, biological functions and structures are still unknown. Two X-ray, structures of a short DNA fragment d(gcGA[G]1Agc) show that four, base-intercalated duplexes are assembled to form an octaplex at a low K+, concentration, in which the eight G5 residues form a stacked double, G-quartet in the central part. At a higher K+ concentration, however, the, octaplex is split into just two halves. These structural features suggest, a folding process of eight tandem repeats of d(ccGA[G]4Agg), according to, a double Greek-key motif. Such a packaging of the repeats could facilitate, slippage of a certain sequence during DNA replication, to induce increase, or decrease of the repeats.
<StructureSection load='1v3n' size='340' side='right'caption='[[1v3n]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1v3n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V3N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V3N FirstGlance]. <br>
</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>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=1v3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v3n OCA], [https://pdbe.org/1v3n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v3n RCSB], [https://www.ebi.ac.uk/pdbsum/1v3n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v3n ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Recent genomic analyses revealed many kinds of tandem repeats of specific sequences. Some of them are related to genetic diseases, but their biological functions and structures are still unknown. Two X-ray structures of a short DNA fragment d(gcGA[G]1Agc) show that four base-intercalated duplexes are assembled to form an octaplex at a low K+ concentration, in which the eight G5 residues form a stacked double G-quartet in the central part. At a higher K+ concentration, however, the octaplex is split into just two halves. These structural features suggest a folding process of eight tandem repeats of d(ccGA[G]4Agg), according to a double Greek-key motif. Such a packaging of the repeats could facilitate slippage of a certain sequence during DNA replication, to induce increase or decrease of the repeats.


==About this Structure==
Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats.,Kondo J, Adachi W, Umeda S, Sunami T, Takenaka A Nucleic Acids Res. 2004 May 7;32(8):2541-9. Print 2004. PMID:15133122<ref>PMID:15133122</ref>
1V3N is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with K as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1V3N OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats., Kondo J, Adachi W, Umeda S, Sunami T, Takenaka A, Nucleic Acids Res. 2004 May 7;32(8):2541-9. Print 2004. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15133122 15133122]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 1v3n" style="background-color:#fffaf0;"></div>
[[Category: Kondo, J.]]
== References ==
[[Category: Sunami, T.]]
<references/>
[[Category: Takenaka, A.]]
__TOC__
[[Category: Umeda, S.]]
</StructureSection>
[[Category: K]]
[[Category: Large Structures]]
[[Category: base-intercalated duplex]]
[[Category: Kondo J]]
[[Category: base-intercalated motif]]
[[Category: Sunami T]]
[[Category: crystal struture]]
[[Category: Takenaka A]]
[[Category: deoxyribonucleic acid]]
[[Category: Umeda S]]
[[Category: dna]]
[[Category: g-duet]]
[[Category: octaplex]]
[[Category: quadruplex]]
[[Category: sheared g:a pair]]
[[Category: x-ray analysis]]
 
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