Summary information

PDB id
1v3p
Class
DNA
Method
X-ray (2.3 Å)
Summary
Crystal structure of d(gcgagagc): the DNA octaplex structure with i-motif of g-quartet
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.
G4 notes
2 G-tetrads, 1 G4 helix

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.115 type=planar nts=4 GGGG 1:A.DG5,3:B.DG13,2:A.DG5,4:B.DG13
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.115 type=planar nts=4 GGGG 1:B.DG13,4:A.DG5,2:B.DG13,3:A.DG5

List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 2 G-tetrad layers, inter-molecular

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG5,3:B.DG13,2:A.DG5,4:B.DG13
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG13,4:A.DG5,2:B.DG13,3:A.DG5
  step#1  mm(<>,outward)  area=27.88 rise=3.53 twist=79.5
  strand#1 DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG5,1:B.DG13
  strand#2 DNA glyco-bond=-- sugar=-- nts=2 GG 3:B.DG13,4:A.DG5
  strand#3 DNA glyco-bond=-- sugar=-- nts=2 GG 2:A.DG5,2:B.DG13
  strand#4 DNA glyco-bond=-- sugar=-- nts=2 GG 4:B.DG13,3:A.DG5

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Interactive view in 3Dmol.js
1 stacking diagram 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG5,3:B.DG13,2:A.DG5,4:B.DG13
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.DG13,4:A.DG5,2:B.DG13,3:A.DG5
  step#1  mm(<>,outward)  area=27.88 rise=3.53 twist=79.5

Download PDB file
Interactive view in 3Dmol.js