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New page: left|200px<br /><applet load="314d" size="350" color="white" frame="true" align="right" spinBox="true" caption="314d, resolution 1.900Å" /> '''Z-DNA HEXAMER WITH ...
 
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[[Image:314d.gif|left|200px]]<br /><applet load="314d" size="350" color="white" frame="true" align="right" spinBox="true"
caption="314d, resolution 1.900&Aring;" />
'''Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WOBBLE BASE PAIR'''<br />


==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]] 1.90&Aring;' 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]] 1.9&#8491;</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>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==About this Structure==
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:9223642<ref>PMID:9223642</ref>
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].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 314d" style="background-color:#fffaf0;"></div>
[[Category: Eichman, B.F.]]
[[Category: Ho, P.S.]]
[[Category: Mooers, B.H.M.]]
[[Category: MG]]
[[Category: NCO]]
[[Category: double helix]]
[[Category: flipped-out base]]
[[Category: overhanging base]]
[[Category: z-dna]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 21:34:54 2008''
==See Also==
*[[Z-DNA|Z-DNA]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Eichman BF]]
[[Category: Ho PS]]
[[Category: Mooers BHM]]

Latest revision as of 08:45, 13 August 2026

Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WOBBLE BASE PAIR

314d, resolution 1.90Å

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