225d

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[[Image:225d.jpg|left|200px]]
 
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{{Structure
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==A TETRAMERIC DNA STRUCTURE WITH PROTONATED CYTOSINE:CYTOSINE BASE PAIRS==
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|PDB= 225d |SIZE=350|CAPTION= <scene name='initialview01'>225d</scene>
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<StructureSection load='225d' size='340' side='right'caption='[[225d]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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<table><tr><td colspan='2'>[[225d]] is a 4 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=225D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=225D 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=225d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=225d OCA], [https://pdbe.org/225d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=225d RCSB], [https://www.ebi.ac.uk/pdbsum/225d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=225d 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=225d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=225d OCA], [http://www.ebi.ac.uk/pdbsum/225d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=225d RCSB]</span>
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== Publication Abstract from PubMed ==
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}}
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'''A TETRAMERIC DNA STRUCTURE WITH PROTONATED CYTOSINE:CYTOSINE BASE PAIRS'''
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==Overview==
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Oligomers containing tracts of cytidine form hemiprotonated base pairs at acid pH and have been considered to be double-stranded. We have solved the structure of the DNA oligomer 5'-d(TCCCCC) at acid pH and find that it is a four-stranded complex in which two base-paired parallel-stranded duplexes are intimately associated, with their base pairs fully intercalated. The relative orientation of the duplexes is antiparallel, so that each base pair is face-to-face with its neighbours. The NMR spectrum displays only six spin systems, showing that the structure is highly symmetrical on the NMR timescale; the four strands are equivalent. A model derived by energy minimization and constrained molecular dynamics shows excellent compatibility with the observed nuclear Overhauser effects (NOEs) particularly for the very unusual inter-residue sugar-sugar NOEs H1'-H1', H1'-H2" and H1'-H4'. These NOEs are probably diagnostic for such tetrameric structures.
Oligomers containing tracts of cytidine form hemiprotonated base pairs at acid pH and have been considered to be double-stranded. We have solved the structure of the DNA oligomer 5'-d(TCCCCC) at acid pH and find that it is a four-stranded complex in which two base-paired parallel-stranded duplexes are intimately associated, with their base pairs fully intercalated. The relative orientation of the duplexes is antiparallel, so that each base pair is face-to-face with its neighbours. The NMR spectrum displays only six spin systems, showing that the structure is highly symmetrical on the NMR timescale; the four strands are equivalent. A model derived by energy minimization and constrained molecular dynamics shows excellent compatibility with the observed nuclear Overhauser effects (NOEs) particularly for the very unusual inter-residue sugar-sugar NOEs H1'-H1', H1'-H2" and H1'-H4'. These NOEs are probably diagnostic for such tetrameric structures.
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==About this Structure==
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A tetrameric DNA structure with protonated cytosine.cytosine base pairs.,Gehring K, Leroy JL, Gueron M Nature. 1993 Jun 10;363(6429):561-5. PMID:8389423<ref>PMID:8389423</ref>
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225D 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=225D OCA].
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==Reference==
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A tetrameric DNA structure with protonated cytosine.cytosine base pairs., Gehring K, Leroy JL, Gueron M, Nature. 1993 Jun 10;363(6429):561-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8389423 8389423]
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[[Category: Protein complex]]
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[[Category: Gehring, K.]]
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[[Category: Gueron, M.]]
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[[Category: Leroy, J L.]]
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[[Category: dna]]
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[[Category: intercalated cytosine tetrad]]
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[[Category: nmr]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:44:36 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 225d" 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: Gehring K]]
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[[Category: Gueron M]]
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[[Category: Leroy JL]]

Current revision

A TETRAMERIC DNA STRUCTURE WITH PROTONATED CYTOSINE:CYTOSINE BASE PAIRS

PDB ID 225d

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