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| - | [[Image:327d.gif|left|200px]] | |
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| - | <!--
| + | ==CRYSTAL STRUCTURES OF D(GM5CGM5CGCGCGC)== |
| - | The line below this paragraph, containing "STRUCTURE_327d", creates the "Structure Box" on the page.
| + | <StructureSection load='327d' size='340' side='right'caption='[[327d]], [[Resolution|resolution]] 1.94Å' 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'>[[327d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=327D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=327D 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]] 1.94Å</td></tr> |
| - | -->
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr> |
| - | {{STRUCTURE_327d| PDB=327d | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=327d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=327d OCA], [https://pdbe.org/327d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=327d RCSB], [https://www.ebi.ac.uk/pdbsum/327d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=327d ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''CRYSTAL STRUCTURES OF D(GM5CGM5CGCGCGC)'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Ramakrishnan B]] |
| - | It is well known that methylation of alternating Py x Pu sequences potentiates the formation of Z-DNA. However, we have now observed that methylation of the alternating Z-DNA oligomer d(GCGCGCGCGC), which starts with a 5'-purine, unexpectedly stabilizes the A-DNA conformation. The double methyl derivative d(Gm5CGm5CGCGCGC), which crystallizes as duplex A-DNA in the hexagonal space group P6(1)22, a = b = 39.33 A and c = 77.93 A with one strand per asymmetric unit and six duplexes in the unit cell, refined to an R factor of 19.1 for 204 DNA atoms and 43 solvent molecules. This is the first report of a DNA sequence crystallized in both right and left-handed conformations, allowing structural comparisons not previously possible and, more importantly, this is the first time that methylation has been shown to potentiate the formation of A-DNA from a sequence known to crystallize as Z-DNA. From this study, ten base-pairs appear to be the critical length in determining the handedness of d(GC)n-type sequences in the crystalline state. Because methylation of nuclear DNA is linked to a number of cellular processes, including transcriptional inactivation, this study has important implications for the role of A-DNA in methylated regions of genomic DNA and, thus, in the regulation of gene expression. In this context, the structure of d(Gm5Cm5CGCGCGC) will be compared with that of the alternating A-DNA decamer d(GCACGCGTGC) and the alternating Z-DNA decamer d(GCGCGCGCGC) and discussed in terms of the forces that govern the handedness of duplex DNA oligomers.
| + | [[Category: Sundaralingam M]] |
| - | | + | [[Category: Tippin DB]] |
| - | ==About this Structure== | + | |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=327D OCA]. | + | |
| - | | + | |
| - | ==Reference== | + | |
| - | Methylation of the Z-DNA decamer d(GC)5 potentiates the formation of A-DNA: crystal structure of d(Gm5CGm5CGCGCGC)., Tippin DB, Ramakrishnan B, Sundaralingam M, J Mol Biol. 1997 Jul 11;270(2):247-58. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9236126 9236126]
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| - | [[Category: Ramakrishnan, B.]] | + | |
| - | [[Category: Sundaralingam, M.]] | + | |
| - | [[Category: Tippin, D B.]]
| + | |
| - | [[Category: A-dna]] | + | |
| - | [[Category: Double helix]] | + | |
| - | [[Category: Modified]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 20:15:53 2008''
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