2fza

[[Image:2fza.gif|left|200px]]<br /><applet load="2fza" size="350" color="white" frame="true" align="right" spinBox="true"

caption="2fza, resolution 3.600&Aring;" />

'''Crystal structure of d(GCGGGAGC): the base-intercalated duplex'''<br />

==Overview==

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.

 

==About this Structure==

2FZA is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FZA OCA].

 

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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16838856 16838856]

[[Category: Ciengshin, T.]]

[[Category: Juan, E.C.M.]]

[[Category: Kondo, J.]]

[[Category: Mitomi, K.]]

[[Category: Takenaka, A.]]

[[Category: base-intercalated duplex]]

[[Category: base-intercalated motif]]

[[Category: deoxyribonucleic acid]]

[[Category: dna]]

[[Category: dna hexaplex]]

[[Category: sheared g:a pair]]