NMR studies on structural features of DNA [d(TCGCGCG)]₂ with a dangling residue T

The DNA heptamer [d(TCGCGCG)]₂, which has an alternating pyrimidine-purine sequence and a dangling T residue at the 5′- end has been used as a model for studying conformational characteristics of DNA duplexes with double-single strand junctions that occur during replication and transcription. The proton resonances of the molecule have been assigned by NOESY and TOCSY/HOHAHA experiments. The NOE intensities at seven different mixing times were quantified for calculating distance constraints with the two-spin approximation. The experiments have uncovered the interesting structural features of the molecule. The sugar proton coupling constants were determined by the P. E. COSY experiment for each residue of the duplex to examine the sugar conformations of the DNA heptamer. The structural features of the heptamer in solution have been obtained. The overall structure of the DNA duplex is basically of a B-type DNA, and substantial changes from a standard B-DNA have been observed, especially in the terminal region of the molecule. The dangling T residue was found in an unusual syn-conformation.