1UE2

Crystal structure of d(GC38GAAAGCT)

Summary for 1UE2

• Entry DOI: 10.2210/pdb1ue2/pdb
• Related: 1UE3 1UE4
• Descriptor: 5'-D(*GP*(C38)P*GP*AP*AP*AP*GP*CP*T)-3', CHLORIDE ION, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: dna, base-intercalated duplex, mini-hairpin structure, sheared g:a pair, zipper-like duplex
• Total number of polymer chains: 1
• Total formula weight: 3111.61

Authors

Sunami, T.,Kondo, J.,Hirao, I.,Watanaba, K.,Miura, K.,Takenaka, A. (deposition date: 2003-05-08, release date: 2004-01-13, Last modification date: 2023-12-27)

Primary citation

Sunami, T.,Kondo, J.,Hirao, I.,Watanabe, K.,Miura, K.I.,Takenaka, A.
Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure.
Acta Crystallogr.,Sect.D, 60:90-96, 2004

PubMed Abstract: 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 G(1)-C(2)-G(3)-A(4)-A(5)(*)-A(5)-A(4)(*)-G(3)(*)-C(2)(*)-G(1)(*) (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(G(Br)CGAAAGCT) and d(G(I)CGAAAGCT), 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 Mg(2+) concentration. The present duplex is preferred under the crystallization conditions, which correspond to physiologically allowed conditions.

PubMed: 14684897
DOI: 10.1107/S0907444903024703

Experimental method

X-RAY DIFFRACTION (1.4 Å)