400d

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[[Image:400d.gif|left|200px]]
 
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==THE INTRINSIC STRUCTURE AND STABILITY OF OUT-OF-ALTERNATION BASE PAIRS IN Z-DNA==
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The line below this paragraph, containing "STRUCTURE_400d", creates the "Structure Box" on the page.
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<StructureSection load='400d' size='340' side='right'caption='[[400d]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[400d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=400D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=400D FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</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=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
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{{STRUCTURE_400d| PDB=400d | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=400d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=400d OCA], [https://pdbe.org/400d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=400d RCSB], [https://www.ebi.ac.uk/pdbsum/400d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=400d ProSAT]</span></td></tr>
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</table>
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'''THE INTRINSIC STRUCTURE AND STABILITY OF OUT-OF-ALTERNATION BASE PAIRS IN Z-DNA'''
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==See Also==
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*[[Z-DNA|Z-DNA]]
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__TOC__
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==Overview==
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</StructureSection>
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Alternating pyrimidine-purine sequences typically form Z-DNA, with the pyrimidines in the anti and purines in the syn conformations. The observation that dC and dT nucleotides can also adopt the syn conformation (i.e. the nucleotides are out-of-alternation) extends the range of sequences that can convert to this left-handed form of DNA. Here, we study the effects of placing two adjacent d(G*C) base pairs as opposed to a single d(G*C) base pair or two d(A*T) base pairs out-of-alternation by comparing the structure of d(m5CGGCm5CG)2with the previously published structures of d(m5CGGGm5CG)*d(m5CGCCm5CG) and d(m5CGATm5CG)2. A high buckle and loss of stacking interactions are observed as intrinsic properties of the out-of-alternation base pairs regardless of sequence and the context of the dinucleotide. From solution titrations, we find that the destabilizing effect of out-of-alternation d(G*C) base pairs are identical whether these base pairs are adjacent or isolated. We can therefore conclude that it is these intrinsic distortions in the structure of the base pairs and not neighboring effects that account for the inability of out-of-alternation base pairs to adopt the left-handed Z conformation.
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[[Category: Large Structures]]
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[[Category: Synthetic construct]]
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==About this Structure==
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[[Category: Basham B]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=400D OCA].
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[[Category: Eichman BF]]
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[[Category: Ho PS]]
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==Reference==
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[[Category: Schroth GP]]
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The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA., Eichman BF, Schroth GP, Basham BE, Ho PS, Nucleic Acids Res. 1999 Jan 15;27(2):543-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9862978 9862978]
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[[Category: Basham, B.]]
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[[Category: Eichman, P S.Ho B F.]]
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[[Category: Schroth, G P.]]
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[[Category: Z-dna double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:15:59 2008''
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Current revision

THE INTRINSIC STRUCTURE AND STABILITY OF OUT-OF-ALTERNATION BASE PAIRS IN Z-DNA

PDB ID 400d

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