1V3O

Crystal structure of d(GCGAGAGC): the DNA quadruplex structure split from the octaplex

Summary for 1V3O

• Entry DOI: 10.2210/pdb1v3o/pdb
• Related: 1V3N 1V3P
• Descriptor: 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3', POTASSIUM ION (3 entities in total)
• Functional Keywords: octaplex, quadruplex, g-duet, base-intercalated duplex, base-intercalated motif, sheared g:a pair, dna, deoxyribonucleic acid, x-ray analysis
• Total number of polymer chains: 2
• Total formula weight: 5244.18

Authors

Kondo, J.,Umeda, S.,Sunami, T.,Takenaka, A. (deposition date: 2003-11-03, release date: 2004-06-08, Last modification date: 2023-10-25)

Primary citation

Kondo, J.,Adachi, W.,Umeda, S.,Sunami, T.,Takenaka, A.
Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats
Nucleic Acids Res., 32:2541-2549, 2004

PubMed Abstract: Recent genomic analyses revealed many kinds of tandem repeats of specific sequences. Some of them are related to genetic diseases, but their biological functions and structures are still unknown. Two X-ray structures of a short DNA fragment d(gcGA[G]1Agc) show that four base-intercalated duplexes are assembled to form an octaplex at a low K+ concentration, in which the eight G5 residues form a stacked double G-quartet in the central part. At a higher K+ concentration, however, the octaplex is split into just two halves. These structural features suggest a folding process of eight tandem repeats of d(ccGA[G]4Agg), according to a double Greek-key motif. Such a packaging of the repeats could facilitate slippage of a certain sequence during DNA replication, to induce increase or decrease of the repeats.

PubMed: 15133122
DOI: 10.1093/nar/gkh575

Experimental method

X-RAY DIFFRACTION (1.7 Å)