Crystal structure of d(GCGAAAGCT) containing parallel-stranded duplex with homo base pairs and anti-parallel duplex with Watson-Crick base pairs.
A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized under a slightly acidic condition, and its crystal structure has been determined at 2.5A resolution. In the first half of the oligomer, the sequence CGAA forms a parallel duplex with another symmetry-related half through the homo base pairs, C2:C2+ (semi-protonated between the Watson-Crick sites), G3:G3 (between the minor groove sites), A4:A4 (between the major groove sites) and A5:A5 (between the Watson-Crick sites). The second halves of the parallel duplex are split away in the different direction, and extended to form an anti-parallel B-form duplex with another second half.
Sunami
Tomoko
T
Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
Kobuna
Tomonori
T
Kondo
Jiro
J
Hirao
Ichiro
I
Watanabe
Kimitsuna
K
Miura
Kin-ichiro
K
Takénaka
Akio
A
D020029:Base Pairing; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation
D004247:DNA