Nucleic Acids Research, 2002, Vol. 30, No. 23 5253-5260
© 2002 Oxford University Press
Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson–Crick base pairs
Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan, 1 RIKEN GSC, Wako-shi 351-0198, Japan, 2 Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904, Japan, 3 Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan and 4 Faculty of Science, Gakushuin University, Tokyo 171-8588, Japan
*To whom correspondence should be addressed. Tel: +81 45 924 5709; Fax: +81 45 924 5748; Email: atakenak{at}bio.titech.ac.jp
A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized in the space group I4122 with the unit-cell dimensions a = b = 53.4 Å and c = 54.0 Å, and the crystal structure has been determined at 2.5 Å resolution. The four nucleotide residues CGAA of the first half of the oligomer form a parallel duplex with another half through the homo base pairs, C2:C2+ (singly-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 two strands remaining in the half of the parallel duplex are split away in different directions, and they pair in an anti-parallel B-form duplex with the second half extending from a neighboring parallel duplex, so that an infinite column is formed in a head-to-tail fashion along the c-axis. It seems that a hexa-ammine cobalt cation supports such a branched and bent conformation of the oligomer. One end of the parallel duplex is stacked on the corresponding end of the adjacent parallel duplex; between them, the guanine base of the first residue is stacked on the fourth ribose of another duplex.
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