1jjp
From Proteopedia
(New page: 200px<br /><applet load="1jjp" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jjp" /> '''A(GGGG) Pentad-Containing Dimeric DNA Quadru...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1jjp.gif|left|200px]]<br /><applet load="1jjp" size=" | + | [[Image:1jjp.gif|left|200px]]<br /><applet load="1jjp" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1jjp" /> | caption="1jjp" /> | ||
'''A(GGGG) Pentad-Containing Dimeric DNA Quadruplex Involving Stacked G(anti)G(anti)G(anti)G(syn) Tetrads'''<br /> | '''A(GGGG) Pentad-Containing Dimeric DNA Quadruplex Involving Stacked G(anti)G(anti)G(anti)G(syn) Tetrads'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We report the results of an NMR study of unlabeled and uniformly | + | 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== | ==About this Structure== | ||
| - | 1JJP is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1JJP is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JJP OCA]. |
==Reference== | ==Reference== | ||
| Line 16: | Line 16: | ||
[[Category: Kettani, A.]] | [[Category: Kettani, A.]] | ||
[[Category: Majumdar, A.]] | [[Category: Majumdar, A.]] | ||
| - | [[Category: Patel, D | + | [[Category: Patel, D J.]] |
[[Category: Skripkin, E.]] | [[Category: Skripkin, E.]] | ||
[[Category: Zhang, N.]] | [[Category: Zhang, N.]] | ||
| Line 25: | Line 25: | ||
[[Category: v-shaped loop and scaffold]] | [[Category: v-shaped loop and scaffold]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:23:26 2008'' |
Revision as of 11:23, 21 February 2008
|
A(GGGG) Pentad-Containing Dimeric DNA Quadruplex Involving Stacked G(anti)G(anti)G(anti)G(syn) Tetrads
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.
About this Structure
1JJP is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Thu Feb 21 13:23:26 2008
