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| {{STRUCTURE_2got| PDB=2got | SCENE= }} | | {{STRUCTURE_2got| PDB=2got | SCENE= }} |
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| '''Crystal structure of d(GCGAACGC): two types of bulge-containing duplexes'''
| | ===Crystal structure of d(GCGAACGC): two types of bulge-containing duplexes=== |
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| ==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.
| | The line below this paragraph, {{ABSTRACT_PUBMED_17505105}}, adds the Publication Abstract to the page |
| | (as it appears on PubMed at http://www.pubmed.gov), where 17505105 is the PubMed ID number. |
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| | {{ABSTRACT_PUBMED_17505105}} |
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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]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 18 12:15:04 2008'' | | |
| | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 02:29:07 2008'' |
