DSSR-PyMOL cartoon-block schematics: PDB entry 1v3n

PDB-id

1v3n; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (1.8 Å)

Summary

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

Reference

Kondo J, Adachi W, Umeda S, Sunami T, Takenaka A (2004): "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. doi: 10.1093/nar/gkh575.

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.