Association of DNA quadruplexes through G:C:G:C tetrads. Solution structure of d(GCGGTGGAT).
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.
Webba da Silva
Mateus
M
Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA. mateus@webbas.org
D001482:Base Composition; D001483:Base Sequence; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D006147:Guanine / Q000737:chemistry*; D006860:Hydrogen Bonding; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D011522:Protons; D011995:Recombination, Genetic; D012965:Sodium Chloride / Q000737:chemistry; D012996:Solutions; D013816:Thermodynamics
D009841:Oligonucleotides; D011522:Protons; D012996:Solutions; D012965:Sodium Chloride; D006147:Guanine; D003596:Cytosine; D004247:DNA