2fza: Difference between revisions

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[[Image:2fza.gif|left|200px]]
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{{STRUCTURE_2fza|  PDB=2fza  |  SCENE=  }}  
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'''Crystal structure of d(GCGGGAGC): the base-intercalated duplex'''
===Crystal structure of d(GCGGGAGC): the base-intercalated duplex===




==Overview==
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DNA fragments with the sequences d(gcGX[Y]n Agc) (n=1, X=A, and Y=A, T, or G)form base-intercalated duplexes, which is a basic unit for formation of multiplexes such as octaplex and hexaplex. To examine the stability of multiplexes, a DNA with X=Y=G and n=1 was crystallized under conditions different from those of the previously determined sequences, and its crystal structure has been determined. The two strands are coupled in an anti-parallel fashion to form a base-intercalated duplex, in which the first and second residues form Watson-Crick type G:C pairs and the third and sixth residues form a sheared G:A pairs at both ends of the duplex. The G4 and G5 bases are stacked alternatively on those of the counter strand to form a long G column of G3-G4-G5*-G5-G4*-G3*, the central four Gs being protruded. In addition, the three duplexes are associated to form a hexaplex around a mixture of calcium and sodium cations on the crystallographic threefold axis. These structural features are similar to those of the previous crystals, though slightly different in detail. The present study indicates that mutation at the 4th position is possible to occur in a base-intercalated duplex for multiplex formations, suggesting that DNA fragments with any sequence sandwiched between the two triplets gcG and Agc can form a multiplex.
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{{ABSTRACT_PUBMED_16838856}}


==About this Structure==
==About this Structure==
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[[Category: Dna hexaplex]]
[[Category: Dna hexaplex]]
[[Category: Sheared g:a pair]]
[[Category: Sheared g:a pair]]
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Revision as of 20:36, 28 July 2008

File:2fza.png

Template:STRUCTURE 2fza

Crystal structure of d(GCGGGAGC): the base-intercalated duplex

Template:ABSTRACT PUBMED 16838856

About this Structure

Full crystallographic information is available from OCA.

Reference

Crystal structure of d(gcGXGAgc) with X=G: a mutation at X is possible to occur in a base-intercalated duplex for multiplex formation., Kondo J, Ciengshin T, Juan EC, Sato Y, Mitomi K, Shimizu S, Takenaka A, Nucleosides Nucleotides Nucleic Acids. 2006;25(4-6):693-704. PMID:16838856

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