NMR observation of a novel C-tetrad in the structure of the SV40 repeat sequence GGGCGG

Biochem Biophys Res Commun. 2000 Apr 21;270(3):967-71. doi: 10.1006/bbrc.2000.2479.


We report the NMR structure of the DNA sequence d-TGGGCGGT in Na(+) solutions at neutral pH, containing a repeat sequence from SV40 viral genome. The structure is a novel quadruplex incorporating the C-tetrad formed by symmetrical pairing of four Cs via NH(2)&bond;O(2) H-bonds in a plane. The C-tetrad has a wider cavity compared to G-tetrads and stacks well over the adjacent G4-tetrad, but poorly on the G6 tetrad. The quadruplex helix is largely underwound by 8-10 degrees compared to B-DNA except at the C5-G6 step. To our knowledge this is the first report of C-tetrad formation in DNA structures, and would be of significance from the point of view of both structural diversity and specific recognition.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA, Viral / chemistry*
  • Genome, Viral
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular / methods
  • Nucleic Acid Conformation
  • Oligodeoxyribonucleotides / chemistry*
  • Repetitive Sequences, Nucleic Acid
  • Simian virus 40 / genetics*


  • DNA, Viral
  • Oligodeoxyribonucleotides