1H NMR studies of a 17-mer DNA duplex

Transcription factor 1 (TF1), encoded by the Bacillus subtilis bacteriophage SPO1, is a DNA-binding protein of the HU family. In preparation for a determination of the structure of the DNA-TF1 complex, we have studied the conformation of one core 17-mer duplex d(5'-CACTACTCTTTGTAGTG-3')-d(5'-CACTACAAAGAGTAGTG-3'). NOESY, DQF-COSY and TOCSY spectroscopy provide resonance assignments of non-exchangeable and exchangeable protons, internucleotide and interstrand proton-proton distances, and dihedral angle constraints. Restrained molecular dynamics calculations yield a family of NMR solution structures for which the RMSD is 0.7 A (all atoms). The helical twist is 34.9 degrees for the central 15 bp. Bends toward the major groove are located between the second and fourth base pairs from each end. The G12 x C23 base pair, which is bounded on each side by consecutive A x T pairs, causes a local disturbance to the DNA helix that makes the conformations of the two end segments unsymmetrical. The pyrimidine rings at T9, T10 and T11 experience more extensive rotational movement than the rest of the structure.