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PDBsum entry 1v3o
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dna_rna metals links
DNA PDB id
1v3o

 

 

 

 

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Contents
DNA/RNA
Metals
__K
Waters ×87
PDB id:
1v3o
Name: DNA
Title: Crystal structure of d(gcgagagc): the DNA quadruplex structure split from the octaplex
Structure: 5'-d( Gp (C38)p Gp Ap Gp Ap Gp C)-3'. Chain: a, b. Engineered: yes
Source: Synthetic: yes
Resolution:
1.70Å     R-factor:   0.262     R-free:   0.296
Authors: J.Kondo,S.Umeda,T.Sunami,A.Takenaka
Key ref: J.Kondo et al. (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. PubMed id: 15133122 DOI: 10.1093/nar/gkh575
Date:
03-Nov-03     Release date:   08-Jun-04    
 Headers
 References

DNA/RNA chains
  G-C38-G-A-G-A-G-C 8 bases
  G-C38-G-A-G-A-G-C 8 bases

 

 
DOI no: 10.1093/nar/gkh575 Nucleic Acids Res 32:2541-2549 (2004)
PubMed id: 15133122  
 
 
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.
J.Kondo, W.Adachi, S.Umeda, T.Sunami, A.Takénaka.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19324891 J.D.Schonhoft, R.Bajracharya, S.Dhakal, Z.Yu, H.Mao, and S.Basu (2009).
Direct experimental evidence for quadruplex-quadruplex interaction within the human ILPR.
  Nucleic Acids Res, 37, 3310-3320.  
18477633 D.Svozil, J.Kalina, M.Omelka, and B.Schneider (2008).
DNA conformations and their sequence preferences.
  Nucleic Acids Res, 36, 3690-3706.  
17505105 J.Kondo, T.Sunami, and A.Takénaka (2007).
The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch.
  Acta Crystallogr D Biol Crystallogr, 63, 673-681.
PDB code: 2got
17389988 P.S.Pallan, P.Lubini, and M.Egli (2007).
A left-handed supramolecular assembly around a right-handed screw axis in the crystal structure of homo-DNA.
  Chem Commun (Camb), (), 1447-1449.  
16714104 A.T.Phan, V.Kuryavyi, and D.J.Patel (2006).
DNA architecture: from G to Z.
  Curr Opin Struct Biol, 16, 288-298.  
16492787 B.Pan, K.Shi, and M.Sundaralingam (2006).
Base-tetrad swapping results in dimerization of RNA quadruplexes: implications for formation of the i-motif RNA octaplex.
  Proc Natl Acad Sci U S A, 103, 3130-3134.
PDB code: 2awe
15324800 M.Egli (2004).
"Deoxyribo nanonucleic acid"; antiparallel, parallel, and unparalleled.
  Chem Biol, 11, 1027-1029.  
15556400 M.Egli (2004).
Nucleic acid crystallography: current progress.
  Curr Opin Chem Biol, 8, 580-591.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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