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| <!-- | | ==Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE HOOGSTEEN BASE PAIR== |
| The line below this paragraph, containing "STRUCTURE_313d", creates the "Structure Box" on the page.
| | <StructureSection load='313d' size='340' side='right'caption='[[313d]], [[Resolution|resolution]] 1.68Å' scene=''> |
| You may change the PDB parameter (which sets the PDB file loaded into the applet)
| | == Structural highlights == |
| or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| | <table><tr><td colspan='2'>[[313d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=313D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=313D FirstGlance]. <br> |
| or leave the SCENE parameter empty for the default display.
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.68Å</td></tr> |
| --> | | <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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr> |
| {{STRUCTURE_313d| PDB=313d | SCENE= }}
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=313d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=313d OCA], [https://pdbe.org/313d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=313d RCSB], [https://www.ebi.ac.uk/pdbsum/313d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=313d ProSAT]</span></td></tr> |
| | </table> |
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| '''Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE HOOGSTEEN BASE PAIR'''
| | ==See Also== |
| | | *[[Z-DNA|Z-DNA]] |
| | | __TOC__ |
| ==Overview== | | </StructureSection> |
| 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.
| | [[Category: Large Structures]] |
| | | [[Category: Eichman BF]] |
| ==About this Structure==
| | [[Category: Ho PS]] |
| Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=313D OCA].
| | [[Category: Mooers BHM]] |
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| ==Reference==
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| 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://www.ncbi.nlm.nih.gov/pubmed/9223642 9223642]
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| [[Category: Eichman, B F.]] | |
| [[Category: Ho, P S.]] | |
| [[Category: Mooers, B H.M.]] | |
| [[Category: Double helix]] | |
| [[Category: Flipped-out base]]
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| [[Category: Modified]]
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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 Sun May 4 20:15:13 2008''
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