Open AccessX‐ray analyses of d(GCGAXAGC) containing G and T at X: the base‐intercalated duplex is still stable even in point mutants at the fifth residue
Author(s) -
Kondo Jiro,
Umeda Shunichi,
Fujita Kazuhiro,
Sunami Tomoko,
Takénaka Akio
Publication year - 2003
Publication title -
journal of synchrotron radiation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.172
H-Index - 99
ISSN - 1600-5775
DOI - 10.1107/s0909049503023562
Subject(s) - duplex (building) , crystallography , residue (chemistry) , base pair , crystal structure , chemistry , mutant , dna , point mutation , stereochemistry , biochemistry , gene
DNA fragments containing the sequence d(GCGAAAGC) prefer to adopt a base‐intercalated (zipper‐like) duplex in the crystalline state. To investigate effects of point mutation at the 5th residue on the structure, two crystal structures of d(GCGAGAGC) and d(GCGATAGC) have been determined by X‐ray crystallography. In the respective crystals, the two octamers related by a crystallographic two‐fold symmetry are aligned in an anti‐parallel fashion and associated to each other to form a duplex, suggesting that the base‐intercalated duplex is stable even when the 5th residue is mutated with other bases. The sheared G 3 :A 6 pair formation makes the two phosphate backbones closer and facilitates formation of the A‐X*‐X‐A* base‐intercalated motif. The three duplexes are assembled around the three‐fold axis, and their 3rd and 4th residues are bound to the hexamine cobalt chloride. The central 5th residues are bound to another cation.