A PSEUDOSQUARE KNOT STRUCTURE OF DNA IN SOLUTION

We report a high-resolution NMR structure of a homodimer formed by a s ynthetic 25 residue DNA oligonucleotide GCTCCCATGGTTTTTGTGCACGAGC. Thi s structure presents a novel structural motif for single-stranded nucl eic acids, called a pseudosquare knot (PSQ). The oligonucleotide was o riginally designed to mimic a slipped-loop structure (SLS), another '' unusual'' DNA structure postulated as an alternative conformation for short direct repeats in double-stranded DNA. The design of the sequenc e is compatible with both SLS and PSQ structures, both of which posses s identical sets of base-paired and unpaired nucleotides but different tertiary folds. We used deuteration of the H8 positions of purines to ascertain that the PSQ is actually formed under the conditions used. The PSQ structure was solved based on homonuclear proton nuclear Overh auser effect data using complete relaxation matrix methods. The struct ure essentially consists of two side-by-side helices connected by sing le-stranded loops. Each of the helices is well-defined; however, the r elative orientation of the two remains undetermined by the NMR data. T he sequences compatible with the PSQ formation are frequent in single- stranded genomes; this structure may play a role as a dimerization mot if.