2FZA

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

Summary for 2FZA

• Entry DOI: 10.2210/pdb2fza/pdb
• Related: 1UE3 1UHX 1V3N 1V3O 1V3P
• Descriptor: 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3', CALCIUM ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: base-intercalated duplex, base-intercalated motif, sheared g:a pair, dna, dna hexaplex, deoxyribonucleic acid
• Total number of polymer chains: 2
• Total formula weight: 5338.18

Authors

Kondo, J.,Ciengshin, T.,Juan, E.C.M.,Mitomi, K.,Takenaka, A. (deposition date: 2006-02-09, release date: 2007-01-23, Last modification date: 2024-03-13)

Primary citation

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

PubMed Abstract: 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.

PubMed: 16838856
DOI: 10.1080/15257770600686543

Experimental method

X-RAY DIFFRACTION (3.6 Å)