Programmable 2D-to-3D structural transformation of DNA nanostructures triggered by single-stranded RNA

Controllable structural transformation of DNA nanostructures offers substantial potential for molecular devices. Toehold-mediated strand displacement, a common strategy for driving such rearrangements, generally requires a dedicated toehold sequence to initiate the reaction, making the regulation of conformational changes in perfectly matched DNA systems challenging. To circumvent this limitation, we herein efficiently assembled a two-dimensional (2D) DNA triangle using only two short DNA strands. Inspired by the structural diversity of RNA, we found that strand displacement induced by the corresponding RNA sequence can alter the assembly pathway of the triangle without a toehold, leading to the formation of a three-dimensional (3D) RNA-DNA hybrid quadrilateral. All nanostructures and their transformation pathways were confirmed by cryogenic-electron microscopy (cryo-EM) and mass spectrometry (MS) analyses. Further, to investigate whether our designed transformable DNA nanostructure can serve as a target-specific signal reporting system, we developed a nucleic acid detection strategy based on isothermal amplification coupled with single-stranded RNA displacement-induced transformation of the DNA nanostructure (SDT), which successfully detected human papillomavirus (HPV) in clinical samples. Our experimental results demonstrate that RNA strand displacement provides new insights into constructing transformable DNA nanostructures and offers a novel design strategy for dynamic DNA nanostructures in molecular diagnostics.