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| | ==Crystal structure of d(GCGAACGC): two types of bulge-containing duplexes== | | ==Crystal structure of d(GCGAACGC): two types of bulge-containing duplexes== |
| - | <StructureSection load='2got' size='340' side='right' caption='[[2got]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='2got' size='340' side='right'caption='[[2got]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2got]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GOT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2got]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GOT FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.602Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ue3|1ue3]], [[1ue4|1ue4]]</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></td></tr> |
| - | <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=2got FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2got OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2got RCSB], [http://www.ebi.ac.uk/pdbsum/2got PDBsum]</span></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=2got FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2got OCA], [https://pdbe.org/2got PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2got RCSB], [https://www.ebi.ac.uk/pdbsum/2got PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2got ProSAT]</span></td></tr> |
| - | <table>
| + | </table> |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | In previous studies, it was reported that DNA fragments with the sequence d(gcGXYAgc) (where X = A or G and Y = A, T or G) form a stable base-intercalated duplex (Bi-duplex) in which the central X and Y residues are not involved in any base-pair interactions but are alternately stacked on each other between the two strands. To investigate the structural stability of the Bi-duplex, the crystal structure of d(gcGAACgc) with a point mutation at the sixth residue of the sequence, d(gcGAAAgc), has been determined. The two strands are associated in an antiparallel fashion to form two types of bulge-containing duplexes (Bc-duplexes), I and II, both of which are quite different from the Bi-duplex of the parent sequence. In both Bc-duplexes, three Watson-Crick G.C base pairs constitute the stem regions at the two ends. The A(4) residues are bulged in to form a pair with the corresponding A(4) residue of the opposite strand in either duplex. The A(4).A(4)* pair formation is correlated to the orientations of the adjacent A(5) residues. A remarkable difference between the two Bc-duplexes is seen at the A(5) residue. In Bc-duplex I, it is flipped out and comes back to interact with the G(3) residue. In Bc-duplex II, the A(5) residue extends outwards to interact with the G(7) residue of the neighbouring Bc-duplex I. These results indicate that trans sugar-edge/Hoogsteen (sheared-type) G(3).A(6)* base pairs are essential in the formation of a Bi-duplex of d(gcGXYAgc). On the other hand, the alternative conformations of the internal loops containing two consecutive bulged A residues suggest molecular switching.
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| - | The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch.,Kondo J, Sunami T, Takenaka A Acta Crystallogr D Biol Crystallogr. 2007 Jun;63(Pt 6):673-81. Epub 2007, May 15. PMID:17505105<ref>PMID:17505105</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div> | + | |
| - | == References ==
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| - | <references/> | + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Kondo, J.]] | + | [[Category: Large Structures]] |
| - | [[Category: Sunami, T.]] | + | [[Category: Kondo J]] |
| - | [[Category: Takenaka, A.]] | + | [[Category: Sunami T]] |
| - | [[Category: Base-intercalated duplex]] | + | [[Category: Takenaka A]] |
| - | [[Category: Bulge-containing duplex]]
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| - | [[Category: Dna]]
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| - | [[Category: Intra-duplex and inter-duplex hand-in-pocket motif]]
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| - | [[Category: Single stranded dna]]
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