The Solution Conformation of a Trisdecanucleotide Containing the Consensus Binding Site of the dnaA Initiation Protein

The solution structure of a trisdecanucleotide, d(CCTGTGGATAACA) · d(TGTTATCCACAGG) containing the consensus binding site of the dnaA initiation protein has been determined by two‐dimensional NMR techniques and restrained molecular dynamics calculations. Interproton distances were obtained by an iterative complete relaxation matrix algorithm, MARDIGRAS. During molecular dynamics runs, the backbone was restricted with the assistance of experimentally derived distance constraints. A family of refined structures with small pairwise root‐mean‐square deviation values (≈0.08 nm) was obtained. All but one of the pyrimidines were found to adopt the C1′‐exo conformation while the purines were found to adopt the C2′‐endo or C1′‐exo conformation. The six‐membered rings of the purines were found to stack over the six‐membered rings of the pyrimidines while there is virtually no overlap of the pyrimidines over the purines. 5′‐purine‐purine‐3′ and 5′‐pyrimidine‐pyrimidine‐3′ stacking resembles the observed stacking of these bases in other NMR and X‐ray structures of oligonucleotides. The final refined structure exhibited a small curvature and was slightly longer than canonical B‐DNA. The variation of twist angle, proposed as a recognition element for proteins, exhibited symmetry about the centre of the consensus binding site.