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1nyd

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[[Image:1nyd.gif|left|200px]]
 
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{{Structure
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==Solution structure of DNA quadruplex GCGGTGGAT==
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|PDB= 1nyd |SIZE=350|CAPTION= <scene name='initialview01'>1nyd</scene>
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<StructureSection load='1nyd' size='340' side='right'caption='[[1nyd]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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<table><tr><td colspan='2'>[[1nyd]] is a 4 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NYD FirstGlance]. <br>
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|ACTIVITY=
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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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|GENE=
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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=1nyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nyd OCA], [https://pdbe.org/1nyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nyd RCSB], [https://www.ebi.ac.uk/pdbsum/1nyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nyd ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=
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<div style="background-color:#fffaf0;">
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nyd OCA], [http://www.ebi.ac.uk/pdbsum/1nyd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nyd RCSB]</span>
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== Publication Abstract from PubMed ==
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}}
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'''Solution structure of DNA quadruplex GCGGTGGAT'''
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==Overview==
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The structure formed by the DNA sequence d(GCGGTGGAT) in a 100 mM Na(+) solution has been determined using molecular dynamics calculations constrained by distance and dihedral restraints derived from NMR experiments performed at isotopic natural abundance. The sequence folds into a dimer of dimers. Each symmetry-related half contains two parallel stranded G:G:G:G tetrads flanked by an A:A mismatch and by four-stranded G:C:G:C tetrads. Each of the two juxtaposed G:C:G:C tetrads is composed of alternating antiparallel strands from the two halves of the dimer. For each single strand, a thymine intersperses a double chain reversal connecting the juxtaposed G:G:G:G tetrads. This architecture has potential implications in genetic recombination. It suggests a pathway for oligomerization involving association of quadruplex entities through GpC steps.
The structure formed by the DNA sequence d(GCGGTGGAT) in a 100 mM Na(+) solution has been determined using molecular dynamics calculations constrained by distance and dihedral restraints derived from NMR experiments performed at isotopic natural abundance. The sequence folds into a dimer of dimers. Each symmetry-related half contains two parallel stranded G:G:G:G tetrads flanked by an A:A mismatch and by four-stranded G:C:G:C tetrads. Each of the two juxtaposed G:C:G:C tetrads is composed of alternating antiparallel strands from the two halves of the dimer. For each single strand, a thymine intersperses a double chain reversal connecting the juxtaposed G:G:G:G tetrads. This architecture has potential implications in genetic recombination. It suggests a pathway for oligomerization involving association of quadruplex entities through GpC steps.
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==About this Structure==
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Association of DNA quadruplexes through G:C:G:C tetrads. Solution structure of d(GCGGTGGAT).,Webba da Silva M Biochemistry. 2003 Dec 16;42(49):14356-65. PMID:14661946<ref>PMID:14661946</ref>
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1NYD is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NYD OCA].
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==Reference==
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Association of DNA quadruplexes through G:C:G:C tetrads. Solution structure of d(GCGGTGGAT)., Webba da Silva M, Biochemistry. 2003 Dec 16;42(49):14356-65. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14661946 14661946]
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[[Category: Protein complex]]
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[[Category: Silva, M Webba da.]]
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[[Category: double chain reversal,dna]]
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[[Category: molecular propeller topology]]
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[[Category: parallel quadruplex]]
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[[Category: quadruplex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:37:12 2008''
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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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<div class="pdbe-citations 1nyd" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Webba da Silva M]]

Current revision

Solution structure of DNA quadruplex GCGGTGGAT

PDB ID 1nyd

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