Association of DNA quadruplexes through G:C:G:C tetrads. Solution structure of d(GCGGTGGAT)

Biochemistry. 2003 Dec 16;42(49):14356-65. doi: 10.1021/bi0355185.


The structure formed by the DNA sequence d(GCGGTGGAT) in a 100 mM Na(+) solution has been determined using molecular dynamics calculations constrained by distance and dihedral restraints derived from NMR experiments performed at isotopic natural abundance. The sequence folds into a dimer of dimers. Each symmetry-related half contains two parallel stranded G:G:G:G tetrads flanked by an A:A mismatch and by four-stranded G:C:G:C tetrads. Each of the two juxtaposed G:C:G:C tetrads is composed of alternating antiparallel strands from the two halves of the dimer. For each single strand, a thymine intersperses a double chain reversal connecting the juxtaposed G:G:G:G tetrads. This architecture has potential implications in genetic recombination. It suggests a pathway for oligomerization involving association of quadruplex entities through GpC steps.

MeSH terms

  • Base Composition
  • Base Sequence
  • Cytosine / chemistry*
  • DNA / chemistry*
  • G-Quadruplexes
  • Guanine / chemistry*
  • Hydrogen Bonding
  • Nuclear Magnetic Resonance, Biomolecular / methods
  • Nucleic Acid Conformation*
  • Oligonucleotides / chemistry*
  • Protons
  • Recombination, Genetic
  • Sodium Chloride / chemistry
  • Solutions
  • Thermodynamics


  • Oligonucleotides
  • Protons
  • Solutions
  • Sodium Chloride
  • Guanine
  • Cytosine
  • DNA