Tuning Geometric Conformation of DNA Nanostructures Using Gaps
摘要
The ability to precisely design the curvature of bent DNA origami structures allows for a wide range of applications in fields such as molecular mechanics. Recent advances have shown that in addition to the insertion or deletion of base pairs, the introduction of nicks or gaps in the phosphate backbone can also effectively tune the curvature of bent DNA origami. Current methods of introducing gaps are limited to tuning the curvature of bent structures by varying the arrangement of the DNA gaps on the origami structure from a single dimension, such as the gap length, which limits the precision of the regulation. Herein, we propose a strategy to precisely tune the structural curvature by adjusting the gap patterns from multiple dimensions. A clamp-like origami structure with gap-tunable units was designed to study the conformational modulation of the bent structure by the gap patterns. By oxDNA simulation, we analyzed the effect of gap length, quantity, and density on the curvature of the structure. This work enhances the design toolbox for DNA nanostructures and provides insights into flexible joint design and DNA damage repair mechanisms.