Dimeric Solution Structure of Two Cyclic Octamers:  Four-Stranded DNA Structures Stabilized by A:T:A:T and G:C:G:C Tetrads

The solution structure of two cyclic octamers of sequence d and d has been determined by two-dimensional NMR spectroscopy and restrained molecular dynamics. The two molecules dimerize at high oligonucleotide concentrations, forming a four-stranded symmetric structure. A complete relaxation matrix analysis of the NOE intensities was carried out, providing a set of around 400 accurate distance constraints. For each oligonucleotide, the calculation converges to very well-defined structures, consisting of two stacks, each with two intermolecular Watson−Crick base pairs. The central residues of each subunit are involved in the base pairs, forming two G:C:G:C or A:T:A:T tetrads, respectively. In both cases, the tetrads are formed by facing the minor groove side of the Watson−Crick base pairs. The tetrads are connected by short loops of two residues. While the residues in the second position of each loop are mainly disordered, nucleotides in the first position (thymines in both cases) are well-defined and form a cap at both ends of the stacks. This is the first time that oligonucleotide structures with minor groove aligned G:C:G:C or A:T:A:T tetrads are observed in solution. Although both oligonucleotides adopt a similar structure, the relative stability of the two molecules is different, with ΔG⁰₂₅ values for dimer formation of −32 and −13 kJ/mol, respectively.