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[[Image:1jjp.gif|left|200px]]


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==A(GGGG) Pentad-Containing Dimeric DNA Quadruplex Involving Stacked G(anti)G(anti)G(anti)G(syn) Tetrads==
The line below this paragraph, containing "STRUCTURE_1jjp", creates the "Structure Box" on the page.
<StructureSection load='1jjp' size='340' side='right'caption='[[1jjp]]' 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'>[[1jjp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JJP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JJP 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">Solution NMR</td></tr>
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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=1jjp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jjp OCA], [https://pdbe.org/1jjp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jjp RCSB], [https://www.ebi.ac.uk/pdbsum/1jjp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jjp ProSAT]</span></td></tr>
{{STRUCTURE_1jjp|  PDB=1jjp  |  SCENE= }}
</table>
 
<div style="background-color:#fffaf0;">
'''A(GGGG) Pentad-Containing Dimeric DNA Quadruplex Involving Stacked G(anti)G(anti)G(anti)G(syn) Tetrads'''
== Publication Abstract from PubMed ==
 
 
==Overview==
We report the results of an NMR study of unlabeled and uniformly (13)C,(15)N-labeled d(G(3)AG(2)T(3)G(3)AT) in 100 mM NaCl, conditions under which it forms a dimeric quadruplex containing several new topological features. The DNA oligomer chain in each symmetry-related monomer subunit undergoes three sharp turns to form a compact domain, with all the purine bases involved in pairing alignments. The first turn is of the double chain reversal type, the second is of the edgewise type, and the third represents a new alignment, the V-shaped type. Each monomer of the dimeric quadruplex contains two stacked G(anti) x G(anti) x G(anti) x G(syn) tetrads, one of which forms a newly identified A x (G x G x G x G) pentad, through sheared G.A mismatch formation. There is a break in one of the four G-G columns that link adjacent G x G x G x G tetrads within each monomer. This architectural interruption is compensated by a new topological feature of quadruplex architecture, the V-shaped scaffold. The missing G-G column results in an opening that could facilitate insertion of planar ligands into the quadruplex. The dimeric interface contains stacked A.(G.G.G.G) pentads, with each pentad containing four bases from one monomer and a syn G1 from the partner monomer. Several potential ligand-binding pockets, positioned towards either end of the folded architecture, were identifiable in a surface view of the solution structure of the dimeric d(G(3)AG(2)T(3)G(3)AT) quadruplex.
We report the results of an NMR study of unlabeled and uniformly (13)C,(15)N-labeled d(G(3)AG(2)T(3)G(3)AT) in 100 mM NaCl, conditions under which it forms a dimeric quadruplex containing several new topological features. The DNA oligomer chain in each symmetry-related monomer subunit undergoes three sharp turns to form a compact domain, with all the purine bases involved in pairing alignments. The first turn is of the double chain reversal type, the second is of the edgewise type, and the third represents a new alignment, the V-shaped type. Each monomer of the dimeric quadruplex contains two stacked G(anti) x G(anti) x G(anti) x G(syn) tetrads, one of which forms a newly identified A x (G x G x G x G) pentad, through sheared G.A mismatch formation. There is a break in one of the four G-G columns that link adjacent G x G x G x G tetrads within each monomer. This architectural interruption is compensated by a new topological feature of quadruplex architecture, the V-shaped scaffold. The missing G-G column results in an opening that could facilitate insertion of planar ligands into the quadruplex. The dimeric interface contains stacked A.(G.G.G.G) pentads, with each pentad containing four bases from one monomer and a syn G1 from the partner monomer. Several potential ligand-binding pockets, positioned towards either end of the folded architecture, were identifiable in a surface view of the solution structure of the dimeric d(G(3)AG(2)T(3)G(3)AT) quadruplex.


==About this Structure==
V-shaped scaffold: a new architectural motif identified in an A x (G x G x G x G) pentad-containing dimeric DNA quadruplex involving stacked G(anti) x G(anti) x G(anti) x G(syn) tetrads.,Zhang N, Gorin A, Majumdar A, Kettani A, Chernichenko N, Skripkin E, Patel DJ J Mol Biol. 2001 Aug 31;311(5):1063-79. PMID:11531340<ref>PMID:11531340</ref>
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JJP OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
V-shaped scaffold: a new architectural motif identified in an A x (G x G x G x G) pentad-containing dimeric DNA quadruplex involving stacked G(anti) x G(anti) x G(anti) x G(syn) tetrads., Zhang N, Gorin A, Majumdar A, Kettani A, Chernichenko N, Skripkin E, Patel DJ, J Mol Biol. 2001 Aug 31;311(5):1063-79. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11531340 11531340]
</div>
[[Category: Chernichenko, N.]]
<div class="pdbe-citations 1jjp" style="background-color:#fffaf0;"></div>
[[Category: Gorin, A.]]
== References ==
[[Category: Kettani, A.]]
<references/>
[[Category: Majumdar, A.]]
__TOC__
[[Category: Patel, D J.]]
</StructureSection>
[[Category: Skripkin, E.]]
[[Category: Large Structures]]
[[Category: Zhang, N.]]
[[Category: Chernichenko N]]
[[Category: Dimeric quadruplex]]
[[Category: Gorin A]]
[[Category: Double chain reversal loop]]
[[Category: Kettani A]]
[[Category: V-shaped loop and scaffold]]
[[Category: Majumdar A]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 21:18:20 2008''
[[Category: Patel DJ]]
[[Category: Skripkin E]]
[[Category: Zhang N]]

Latest revision as of 18:43, 29 November 2023

A(GGGG) Pentad-Containing Dimeric DNA Quadruplex Involving Stacked G(anti)G(anti)G(anti)G(syn) Tetrads

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