'''Crystal structure of d(GCGAACGC): two types of bulge-containing duplexes'''
===Crystal structure of d(GCGAACGC): two types of bulge-containing duplexes===
==Overview==
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In previous studies, it was reported that DNA fragments with the sequence d(gcGXYAgc) (where X = A or G and Y = A, T or G) form a stable base-intercalated duplex (Bi-duplex) in which the central X and Y residues are not involved in any base-pair interactions but are alternately stacked on each other between the two strands. To investigate the structural stability of the Bi-duplex, the crystal structure of d(gcGAACgc) with a point mutation at the sixth residue of the sequence, d(gcGAAAgc), has been determined. The two strands are associated in an antiparallel fashion to form two types of bulge-containing duplexes (Bc-duplexes), I and II, both of which are quite different from the Bi-duplex of the parent sequence. In both Bc-duplexes, three Watson-Crick G.C base pairs constitute the stem regions at the two ends. The A(4) residues are bulged in to form a pair with the corresponding A(4) residue of the opposite strand in either duplex. The A(4).A(4)* pair formation is correlated to the orientations of the adjacent A(5) residues. A remarkable difference between the two Bc-duplexes is seen at the A(5) residue. In Bc-duplex I, it is flipped out and comes back to interact with the G(3) residue. In Bc-duplex II, the A(5) residue extends outwards to interact with the G(7) residue of the neighbouring Bc-duplex I. These results indicate that trans sugar-edge/Hoogsteen (sheared-type) G(3).A(6)* base pairs are essential in the formation of a Bi-duplex of d(gcGXYAgc). On the other hand, the alternative conformations of the internal loops containing two consecutive bulged A residues suggest molecular switching.
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==About this Structure==
==About this Structure==
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[[Category: Single stranded dna]]
[[Category: Single stranded dna]]
[[Category: X-ray structure]]
[[Category: X-ray structure]]
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Revision as of 23:29, 27 July 2008
This article has been automatically seeded. Changes to this page should pertain to the PDB entry only and not to the protein or biomolecule in general.
2GOT is a Single protein structure. Full crystallographic information is available from OCA.
Reference
The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch., Kondo J, Sunami T, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2007 Jun;63(Pt 6):673-81. Epub 2007, May 15. PMID:17505105
