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| - | [[Image:376d.gif|left|200px]] | |
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| - | <!--
| + | ==A ZIPPER-LIKE DNA DUPLEX D(GCGAAAGCT)== |
| - | The line below this paragraph, containing "STRUCTURE_376d", creates the "Structure Box" on the page.
| + | <StructureSection load='376d' size='340' side='right'caption='[[376d]], [[Resolution|resolution]] 2.10Å' 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'>[[376d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=376D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=376D 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]] 2.1Å</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=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr> |
| - | {{STRUCTURE_376d| PDB=376d | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=376d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=376d OCA], [https://pdbe.org/376d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=376d RCSB], [https://www.ebi.ac.uk/pdbsum/376d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=376d ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''A ZIPPER-LIKE DNA DUPLEX D(GCGAAAGCT)'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Cruse WBT]] |
| - | BACKGROUND: The replication origin of the single-stranded (ss)DNA bacteriophage G4 has been proposed to fold into a hairpin loop containing the sequence GCGAAAGC. This sequence comprises a purine-rich motif (GAAA), which also occurs in conserved repetitive sequences of centromeric DNA. ssDNA analogues of these sequences often show exceptional stability which is associated with hairpin loops or unusual duplexes, and may be important in DNA replication and centromere function. Nuclear magnetic resonance (NMR) studies indicate that the GCGAAAGC sequence forms a hairpin loop in solution, while centromere-like repeats dimerise into unusual duplexes. The factors stabilising these unusual secondary structure elements in ssDNA, however, are poorly understood. RESULTS: The nonamer d(GCGAAAGCT) was crystallised as a bromocytosine derivative in the presence of cobalt hexammine. The crystal structure, solved by the multiple wavelength anomalous dispersion (MAD) method at the bromine K-edge, reveals an unexpected zipper-like motif in the middle of a standard B-DNA duplex. Four central adenines, flanked by two sheared G.A mismatches, are intercalated and stacked on top of each other without any interstrand Watson-Crick base pairing. The cobalt hexammine cation appears to participate only in crystal cohesion. CONCLUSIONS: The GAAA consensus sequence can dimerise into a stable zipper-like duplex as well as forming a hairpin loop. The arrangement closes the minor groove and exposes the intercalated, unpaired, adenines to the solvent and DNA-binding proteins. Such a motif, which can transform into a hairpin, should be considered as a structural option in modelling DNA and as a potential binding site, where it could have a role in DNA replication, nuclease resistance, ssDNA genome packaging and centromere function.
| + | [[Category: Fourme R]] |
| - | | + | [[Category: Prange T]] |
| - | ==About this Structure== | + | [[Category: Shepard W]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=376D OCA]. | + | [[Category: DelalFortelle E]] |
| - | | + | |
| - | ==Reference== | + | |
| - | A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution., Shepard W, Cruse WB, Fourme R, de la Fortelle E, Prange T, Structure. 1998 Jul 15;6(7):849-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9687367 9687367]
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| - | [[Category: Cruse, W B.T.]] | + | |
| - | [[Category: Fourme, R.]] | + | |
| - | [[Category: Prange, T.]] | + | |
| - | [[Category: Shepard, W.]] | + | |
| - | [[Category: DelalFortelle, E.]] | + | |
| - | [[Category: Double helix]] | + | |
| - | [[Category: Mismatched]] | + | |
| - | [[Category: Modified]] | + | |
| - | [[Category: Overhanging base]] | + | |
| - | [[Category: Right handed dna]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 20:17:52 2008''
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