Characteristics of specific DNA junction motifs inspired by natural RNA motifs

DNA junction motifs play critical roles in biological activities and precise DNA nanoconstruction. However, the relationship between the sequence of junction motifs and their structural characteristics remains unclear. Herein we designed a specific DNA three-way junction (D3) motif and a DNA kink-turn (DK) motif by mimicking natural RNA motifs. Through tile/motif-based self-assembly strategy, we systematically investigated the sequences and structural characteristics of these two specific DNA motifs. Our experimental results demonstrate that the D3 motif can form a 60° angle, similar to natural RNA structures, while the DK motif forms a 60° angle instead of the 90° angle observed in natural RNA. Both motifs can further assemble into DNA triangular structures. Further, we found that the number of unpaired nucleotides at the junction region significantly influences the geometric angles and flexibility of these DNA motifs. Specifically, a reduction in unpaired nucleotides increases the geometric interstrand angle, and the originally rigid 60° DNA motif becomes flexible to self-assemble into quadrilateral and pentagonal structures with 90° and 108° angles, respectively. Our study reveals fundamental relationships between the number of unpaired nucleotides and the structural characteristics of DNA junction motifs, providing important guidance for the precise and efficient assembly of DNA nanostructures.