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| - | [[Image:2fza.gif|left|200px]] | |
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| - | <!--
| + | ==Crystal structure of d(GCGGGAGC): the base-intercalated duplex== |
| - | The line below this paragraph, containing "STRUCTURE_2fza", creates the "Structure Box" on the page.
| + | <StructureSection load='2fza' size='340' side='right'caption='[[2fza]], [[Resolution|resolution]] 3.60Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[2fza]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FZA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FZA FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.6Å</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | {{STRUCTURE_2fza| PDB=2fza | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fza OCA], [https://pdbe.org/2fza PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fza RCSB], [https://www.ebi.ac.uk/pdbsum/2fza PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fza ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''Crystal structure of d(GCGGGAGC): the base-intercalated duplex'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Ciengshin T]] |
| - | DNA fragments with the sequences d(gcGX[Y]n Agc) (n=1, X=A, and Y=A, T, or G)form base-intercalated duplexes, which is a basic unit for formation of multiplexes such as octaplex and hexaplex. To examine the stability of multiplexes, a DNA with X=Y=G and n=1 was crystallized under conditions different from those of the previously determined sequences, and its crystal structure has been determined. The two strands are coupled in an anti-parallel fashion to form a base-intercalated duplex, in which the first and second residues form Watson-Crick type G:C pairs and the third and sixth residues form a sheared G:A pairs at both ends of the duplex. The G4 and G5 bases are stacked alternatively on those of the counter strand to form a long G column of G3-G4-G5*-G5-G4*-G3*, the central four Gs being protruded. In addition, the three duplexes are associated to form a hexaplex around a mixture of calcium and sodium cations on the crystallographic threefold axis. These structural features are similar to those of the previous crystals, though slightly different in detail. The present study indicates that mutation at the 4th position is possible to occur in a base-intercalated duplex for multiplex formations, suggesting that DNA fragments with any sequence sandwiched between the two triplets gcG and Agc can form a multiplex.
| + | [[Category: Juan ECM]] |
| - | | + | [[Category: Kondo J]] |
| - | ==About this Structure== | + | [[Category: Mitomi K]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FZA OCA]. | + | [[Category: Takenaka A]] |
| - | | + | |
| - | ==Reference== | + | |
| - | Crystal structure of d(gcGXGAgc) with X=G: a mutation at X is possible to occur in a base-intercalated duplex for multiplex formation., Kondo J, Ciengshin T, Juan EC, Sato Y, Mitomi K, Shimizu S, Takenaka A, Nucleosides Nucleotides Nucleic Acids. 2006;25(4-6):693-704. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16838856 16838856]
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| - | [[Category: Ciengshin, T.]]
| + | |
| - | [[Category: Juan, E C.M.]] | + | |
| - | [[Category: Kondo, J.]]
| + | |
| - | [[Category: Mitomi, K.]] | + | |
| - | [[Category: Takenaka, A.]] | + | |
| - | [[Category: Base-intercalated duplex]] | + | |
| - | [[Category: Base-intercalated motif]] | + | |
| - | [[Category: Deoxyribonucleic acid]] | + | |
| - | [[Category: Dna]] | + | |
| - | [[Category: Dna hexaplex]] | + | |
| - | [[Category: Sheared g:a pair]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 04:29:13 2008''
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