Interlocked mismatch-aligned arrowhead DNA motifs

Background: Triplet repeat sequences are of considerable biological importance as the expansion of such tandem arrays can lead to the onset of a range of human diseases. Such sequences can self-pair via mismatch alignments to form higher order structures that have the potential to cause replication blocks, followed by strand slippage and sequence expansion. The all-purine d(GGA)(n) triplet repeat sequence is of particular interest because purines can align via G·G₁ A·A and G·A mismatch formation. Results: We have solved the structure of the uniformly ¹³C,¹⁵N-labeled d(G1-G2-A3-G4-GS- A6-T7) sequence in 10 mM Na⁺ solution. This sequence adopts a novel twofold- symmetric duplex fold where interlocked V-shaped arrowhead motifs are aligned solely via interstrand G1·G4₁ G2·G5 and A3·A6 mismatch formation. The tip of the arrowhead motif is centered about the p-A3-p step, and symmetry- related local parallel-stranded duplex domains are formed by the G1-G2-A3 and G4-G5-A6 segments of partner strands. Conclusions: The purine-rich (GGA)(n) triplet repeat sequence is dispersed throughout the eukaryotic genome. Several features of the arrowhead duplex motif for the (GGA)₂ triplet repeat provide a unique scaffold for molecular recognition. These include the large localized bend in the sugar-phosphate backbones, the segmental parallel- stranded alignment of strands and the exposure of the Watson-Crick edges of several mismatched bases.