PDBsum entry 1mf5

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PDB id:
Name: DNA
Title: Gcatgct quadruplex
Structure: 5'-d( Gp Cp Ap Tp Gp Cp T)-3'. Chain: a, b. Engineered: yes
Source: Synthetic: yes
1.10Å     R-factor:   0.216     R-free:   0.224
Authors: J.H.Thorpe,S.C.M.Teixeira,B.C.Gale,C.J.Cardin
Key ref: J.H.Thorpe et al. (2003). Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution. Nucleic Acids Res, 31, 844-849. PubMed id: 12560479 DOI: 10.1093/nar/gkg168
09-Aug-02     Release date:   11-Feb-03    


DOI no: 10.1093/nar/gkg168 Nucleic Acids Res 31:844-849 (2003)
PubMed id: 12560479  
Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution.
J.H.Thorpe, S.C.Teixeira, B.C.Gale, C.J.Cardin.
Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 A. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19621410 L.A.Howell, and M.Searcey (2009).
Targeting higher-order DNA: beyond the G-quadruplex.
  Chembiochem, 10, 2139-2143.  
16607659 N.Escaja, I.Gómez-Pinto, J.Viladoms, M.Rico, E.Pedroso, and C.González (2006).
Induced-fit recognition of DNA by small circular oligonucleotides.
  Chemistry, 12, 4035-4042.  
15556400 M.Egli (2004).
Nucleic acid crystallography: current progress.
  Curr Opin Chem Biol, 8, 580-591.  
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