1IXJ

Crystal Structure of d(GCGAAAGCT) Containing Parallel-stranded Duplex with Homo Base Pairs and Anti-Parallel Duplex with Watson-Crick Base pairs

Summary for 1IXJ

• Entry DOI: 10.2210/pdb1ixj/pdb
• Descriptor: 5'-D(*GP*CP*GP*AP*AP*AP*GP*CP*T)-3', MAGNESIUM ION, COBALT HEXAMMINE(III), ... (4 entities in total)
• Functional Keywords: parallel dna, homo base pairs, parallel-stranded helix, parallel duplex, dna
• Total number of polymer chains: 1
• Total formula weight: 2974.56

Authors

Sunami, T.,Kondo, J.,Kobuna, T.,Hirao, I.,Watanabe, K.,Miura, K.,Takenaka, A. (deposition date: 2002-06-22, release date: 2002-12-11, Last modification date: 2023-12-27)

Primary citation

Sunami, T.,Kondo, J.,Kobuna, T.,Hirao, I.,Watanabe, K.,Miura, K.,Takenaka, A.
Crystal Structure of d(GCGAAAGCT) Containing a Parallel-stranded Duplex with Homo Base Pairs and an Anti-Parallel Duplex with Watson-Crick Base pairs
Nucleic Acids Res., 30:5253-5260, 2002

PubMed Abstract: A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized in the space group I4(1)22 with the unit-cell dimensions a = b = 53.4 A and c = 54.0 A, and the crystal structure has been determined at 2.5 A 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.

PubMed: 12466550
DOI: 10.1093/nar/gkf639

Experimental method

X-RAY DIFFRACTION (2.5 Å)