184d
From Proteopedia
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SELF-ASSOCIATION OF A DNA LOOP CREATES A QUADRUPLEX: CRYSTAL STRUCTURE OF D(GCATGCT) AT 1.8 ANGSTROMS RESOLUTION
Overview
BACKGROUND: The flexibility of DNA enables it to adopt three, interconvertible types of duplex termed the A-, B- and Z-forms. It can, also produce hairpin loops, triplex structures and guanine-rich quadruplex, structures. Conformational flexibility assists in the tight packaging of, DNA, for example in chromosomes. This is important given the large, quantity of genetic information that must be packaged efficiently., Moreover, the ability of DNA to specifically self-associate or interact, with complementary sequences is fundamental to many biological processes., Structural studies provide information about DNA conformation and DNA-DNA, interactions and suggest features that might be relevant to how the, molecule performs its biological role. RESULTS: We have characterized the, structure of a synthetic heptanucleotide that folds into a novel loop, structure. The loop is stabilized by association with a cation, by, intra-strand hydrogen bonds between guanine and cytosine that are distinct, from the normal Watson-Crick hydrogen bonds, and by van der Waals, interactions. Two loops associate through the formation of four G.C pairs, that exhibit pronounced base-stacking interactions. The formation of a, symmetric A.A base pair further stabilizes loop dimerization. Stacking of, the A.A pair on a symmetry-related A.A pairing assists the formation of a, four-stranded assembly. A T.T pairing is also observed between, symmetry-related loops. CONCLUSIONS: This analysis provides a rare example, of an experimentally determined non-duplex DNA structure. It provides, conformational detail relevant to the tight packaging or folding of a DNA, strand and illustrates how a cation might modulate phosphate-phosphate, repulsion in a tightly packed structure. The observation of base quartets, involving G.C base pairs suggests a further structure to be considered in, DNA-DNA interactions. The structure also provides detailed geometries for, A.A and T.T base pairs.
About this Structure
184D is a Protein complex structure of sequences from [1] with MG as ligand. Full crystallographic information is available from OCA.
Reference
Self-association of a DNA loop creates a quadruplex: crystal structure of d(GCATGCT) at 1.8 A resolution., Leonard GA, Zhang S, Peterson MR, Harrop SJ, Helliwell JR, Cruse WB, d'Estaintot BL, Kennard O, Brown T, Hunter WN, Structure. 1995 Apr 15;3(4):335-40. PMID:7613864
Page seeded by OCA on Sat Nov 24 22:08:45 2007
