NMR observation of a novel C-tetrad in the structure of the SV40 repeat sequence GGGCGG.
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.
Patel
P K
PK
Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India.
Bhavesh
N S
NS
Hosur
R V
RV
D001483:Base Sequence; D004279:DNA, Viral / Q000737:chemistry*; D016679:Genome, Viral; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D012091:Repetitive Sequences, Nucleic Acid; D013539:Simian virus 40 / Q000235:genetics*
D004279:DNA, Viral; D009838:Oligodeoxyribonucleotides