312d: Difference between revisions
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==Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIR== | ==Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIR== | ||
<StructureSection load='312d' size='340' side='right' caption='[[312d]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='312d' size='340' side='right' caption='[[312d]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
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<table><tr><td colspan='2'>[[312d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=312D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=312D FirstGlance]. <br> | <table><tr><td colspan='2'>[[312d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=312D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=312D FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=312d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=312d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=312d RCSB], [http://www.ebi.ac.uk/pdbsum/312d PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=312d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=312d OCA], [http://pdbe.org/312d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=312d RCSB], [http://www.ebi.ac.uk/pdbsum/312d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=312d ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 312d" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 22:32, 11 August 2016
Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIRZ-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIR
Structural highlights
Publication Abstract from PubMedWe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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