1jjp
From Proteopedia
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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
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