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From Proteopedia
Crystal structure of d(GCGAGAGC): the base-intercalated duplex
Overview
DNA fragments containing the sequence d(GCGAAAGC) prefer to adopt a base-intercalated (zipper-like) duplex in the crystalline state. To investigate effects of point mutation at the 5th residue on the structure, two crystal structures of d(GCGAGAGC) and d(GCGATAGC) have been determined by X-ray crystallography. In the respective crystals, the two octamers related by a crystallographic two-fold symmetry are aligned in an anti-parallel fashion and associated to each other to form a duplex, suggesting that the base-intercalated duplex is stable even when the 5th residue is mutated with other bases. The sheared G3:A6 pair formation makes the two phosphate backbones closer and facilitates formation of the A-X*-X-A* base-intercalated motif. The three duplexes are assembled around the three-fold axis, and their 3rd and 4th residues are bound to the hexamine cobalt chloride. The central 5th residues are bound to another cation.
About this Structure
Full crystallographic information is available from OCA.
Reference
X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue., Kondo J, Umeda S, Fujita K, Sunami T, Takenaka A, J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):117-20. Epub 2003 Nov 28. PMID:14646150 Page seeded by OCA on Sat May 3 11:15:27 2008
