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Base-intercalated Duplex (base-intercalated + duplex)

Distribution by Scientific Domains
Chemistry100%

Selected Abstracts

X-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

JOURNAL OF SYNCHROTRON RADIATION, Issue 1 2004
Jiro Kondo
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 G3:A6 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. [source]

Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2004
d(GCGAAAGC)
A DNA fragment d(GCGAAAGC), postulated to adopt a stable mini-hairpin structure on the basis of its extraordinary properties, has been X-ray analyzed. Two octamers related by a crystallographic twofold symmetry are aligned in an antiparallel fashion and associate to form a duplex, which is maintained by two Watson,Crick G·C base pairs and a subsequent sheared G·A pair at both ends. The central two A residues are free from base-pair formation. The corresponding base moieties of the two strands are intercalated and stacked on each other, forming a long column of G1 -C2 -G3 -A4 -A -A5 -A -G -C -G (asterisks indicate the counter-strand). The Watson,Crick and major-groove sites of the four stacked adenine bases are exposed to the solvent region, suggesting a functional role. Since this structural motif is similar to those found in the nonamers d(GBrCGAAAGCT) and d(GICGAAAGCT), the base-intercalated duplex may be a stable form of the specific sequence. Electrophoresis results suggest that the octamer has two states, monomeric and dimeric, in solution depending on the Mg2+ concentration. The present duplex is preferred under the crystallization conditions, which correspond to physiologically allowed conditions. [source]