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| [[Image:314d.gif|left|200px]]<br /><applet load="314d" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="314d, resolution 1.900Å" />
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| '''Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WOBBLE BASE PAIR'''<br />
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| ==Overview== | | ==Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WOBBLE BASE PAIR== |
| We have solved the structures of the homoduplex d(Gm5CGCGCG)2, and the, heteroduplexes d(GCGCGCG)/d(TCGCGCG) and d(GCGCGCG)/d(CCGCGCG). The, structures form six base-pairs of identical Z-DNA duplexes with single, nucleotides overhanging at the 5'-ends. The overhanging nucleotide from, one strand remains stacked and sandwiched between the blunt-ends of two, adjacent Z-DNA duplexes, while the overhanging base of the opposing strand, is extra-helical. The stacked and the extra-helical bases from adjacent, duplexes pair to form a distorted d(G x G) reverse Hoogsteen base-pair in, the d(Gm5CGCGCG)2 homoduplex, and d(G x T) reverse wobble and d(G x C), reverse Watson-Crick base-pairs in the d(GCGCGCG)/d(TCGCGCG) and, d(GCGCGCG)/d(CCGCGCG) heteroduplexes, respectively. Interestingly, only, the d(G,T) and d(G x C) base-pairs were observed in the heteroduplexes, suggesting that both the d(G x T) reverse wobble and d(G x C) reverse, Watson-Crick base-pairs are more stable in this crystal environment than, the d(G x G) reverse Hoogsteen base-pair. To estimate the relative, stability of the three types of reverse base-pairs, crystals were grown, using various mixtures of sequences and their strand compositions analyzed, by mass spectrometry. The d(G x C) reverse Watson-Crick base-pair was, estimated to be more stable by approximately 1.5 kcal/mol and the d(G x T), reverse wobble base-pair more stable by approximately 0.5 kcal/mol than, the d(G x G) reverse Hoogsteen base-pair. The step during crystallization, responsible for discriminating between the strands in the crystal is, highly cooperative, suggesting that it occurs during the initial, nucleating event of crystal growth.
| | <StructureSection load='314d' size='340' side='right'caption='[[314d]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == |
| | <table><tr><td colspan='2'>[[314d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=314D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=314D FirstGlance]. <br> |
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr> |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=314d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=314d OCA], [https://pdbe.org/314d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=314d RCSB], [https://www.ebi.ac.uk/pdbsum/314d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=314d ProSAT]</span></td></tr> |
| | </table> |
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| ==About this Structure== | | ==See Also== |
| 314D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=NCO:'>NCO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=314D OCA].
| | *[[Z-DNA|Z-DNA]] |
| | | __TOC__ |
| ==Reference==
| | </StructureSection> |
| The structures and relative stabilities of d(G x G) reverse Hoogsteen, d(G x T) reverse wobble, and d(G x C) reverse Watson-Crick base-pairs in DNA crystals., Mooers BH, Eichman BF, Ho PS, J Mol Biol. 1997 Jun 27;269(5):796-810. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9223642 9223642]
| | [[Category: Large Structures]] |
| [[Category: Protein complex]] | | [[Category: Eichman BF]] |
| [[Category: Eichman, B.F.]] | | [[Category: Ho PS]] |
| [[Category: Ho, P.S.]] | | [[Category: Mooers BHM]] |
| [[Category: Mooers, B.H.M.]] | |
| [[Category: MG]]
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| [[Category: NCO]]
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| [[Category: double helix]]
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| [[Category: flipped-out base]]
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| [[Category: overhanging base]]
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| [[Category: z-dna]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 21:34:54 2008''
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