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| - | [[Image:1p4z.gif|left|200px]] | |
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| - | <!--
| + | ==Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions== |
| - | The line below this paragraph, containing "STRUCTURE_1p4z", creates the "Structure Box" on the page.
| + | <StructureSection load='1p4z' size='340' side='right'caption='[[1p4z]], [[Resolution|resolution]] 2.00Å' 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'>[[1p4z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P4Z 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]] 2Å</td></tr> |
| - | -->
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | {{STRUCTURE_1p4z| PDB=1p4z | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1p4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4z OCA], [https://pdbe.org/1p4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p4z RCSB], [https://www.ebi.ac.uk/pdbsum/1p4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4z ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Hays FA]] |
| - | Structures of the DNA sequences d(CCGGCGCCGG) and d(CCAGTACbr(5)UGG) are presented here as four-way Holliday junctions in their compact stacked-X forms, with antiparallel alignment of the DNA strands. Thus, the ACC-trinucleotide motif, previously identified as important for stabilizing the junction, is now extended to PuCPy, where Pu is either an adenine or guanine, and Py is either a cytosine, 5-methylcytosine, or 5-bromouracil but not thymine nucleotide. We see that both sequence and base substituents affect the geometry of the junction in terms of the interduplex angle as well as the previously defined conformational variables, J(roll) (the rotation of the stacked duplexes about their respective helical axis) and J(slide) (the translational displacement of the stacked duplexes along their respective helical axis). The structures of the GCC and parent ACC containing junctions fall into a distinct conformational class that is relatively undistorted in terms of J(slide) and J(roll), with interduplex angles of 40-43 degrees. The substituted ACbr(5)U structure, however, is more akin to that of the distorted methylated ACm(5)C containing junction, with J(slide) (>or=2.3 A) and a similar J(roll) (164 degrees) opening the major groove-side of the junction, but shows a reduced interduplex angle. In contrast, the analogous d(CCAGTACTGG) sequence has to date been crystallized only as resolved B-DNA duplexes. This suggests that there is an electronic effect of substituents at the pyrimidine Py position on the stability of four-stranded junctions. The single-crystal structures presented here, therefore, show how sequence affects the detailed geometry, and subsequently, the associated stability and conformational dynamics of the Holliday junction.
| + | [[Category: Ho PS]] |
| - | | + | [[Category: Vargason JM]] |
| - | ==About this Structure== | + | |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4Z OCA]. | + | |
| - | | + | |
| - | ==Reference== | + | |
| - | Effect of sequence on the conformation of DNA holliday junctions., Hays FA, Vargason JM, Ho PS, Biochemistry. 2003 Aug 19;42(32):9586-97. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12911300 12911300]
| + | |
| - | [[Category: Hays, F A.]] | + | |
| - | [[Category: Ho, P S.]] | + | |
| - | [[Category: Vargason, J M.]] | + | |
| - | [[Category: B-dna]] | + | |
| - | [[Category: Double helix]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 04:41:39 2008''
| + | |
