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| - | [[Image:327d.gif|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTAL STRUCTURES OF D(GM5CGM5CGCGCGC)== |
| - | |PDB= 327d |SIZE=350|CAPTION= <scene name='initialview01'>327d</scene>, resolution 1.940Å
| + | <StructureSection load='327d' size='340' side='right'caption='[[327d]], [[Resolution|resolution]] 1.94Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=5CM:5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene> | + | <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> |
| - | |ACTIVITY=
| + | </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> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=327d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=327d OCA], [http://www.ebi.ac.uk/pdbsum/327d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=327d RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''CRYSTAL STRUCTURES OF D(GM5CGM5CGCGCGC)'''
| + | [[Category: Ramakrishnan B]] |
| - | | + | [[Category: Sundaralingam M]] |
| - | | + | [[Category: Tippin DB]] |
| - | ==Overview==
| + | |
| - | 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.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 327D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=327D OCA].
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| - | | + | |
| - | ==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: Protein complex]] | + | |
| - | [[Category: Ramakrishnan, B.]] | + | |
| - | [[Category: Sundaralingam, M.]] | + | |
| - | [[Category: Tippin, D B.]] | + | |
| - | [[Category: a-dna]]
| + | |
| - | [[Category: double helix]]
| + | |
| - | [[Category: modified]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:21:24 2008''
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